In 1963, after he'd been making films for 11 years, Stan Brakhage published his first book on cinema, Metaphors on Vision. This was long before he and Eisenstein were paired in a special issue of Artforum; before he'd been offered any teaching jobs; before any schools or film museums had bought prints of his films; before the first comprehensive retrospective of his work at New York's Museum of Modern Art. Back then he was almost completely excluded from "film culture," save for a few articles about his work in a low-circulation periodical of that name. Long before Apple used the phrase "think different" to sell its computers, he saw the world and cinema very differently from mainstream America, which was still closer in feeling at that time to the Eisenhower era than to the chaotic late 60s. Back then, only a few years after the birth of his first child, he began Metaphors on Vision by writing: "Imagine an eye unruled by man-made laws of perspective, an eye unprejudiced by compositional logic, an eye which does not respond to the name of everything but which must know each object encountered in life through an adventure of perception. How many colors are there in a field of grass to the crawling baby unaware of 'Green'?"

Today, despite Brakhage's stature as perhaps America's best-known avant-garde or experimental filmmaker and not withstanding the fact that he's still making great films, his work is rarely screened and even more rarely understood. For over a decade, beginning in 1970, he flew in from Colorado — where he's lived most of his adult life — to lecture on film aesthetics and history at the School of the Art Institute, where his talks were widely attended; Studs Terkel had him on the radio more than once. Yet I know of only three one-person shows of new work in Chicago since the early 80s — and one of them is the program of six abstract films, mostly from 1999, presented by Chicago Filmmakers Friday night at Columbia College. Few of his films from the last two decades have ever been shown here, though they've all been shown at least once in New York. Fame in the world of avant-garde film still doesn't amount to much; Brakhage has never been able to support himself through filmmaking.

His work is not easy to like. Most of his films are silent: Brakhage argues that the viewer will be better attuned to the rhythms of the imagery without a sound track. In recent years, most of his films have been abstract. And the elements that have given some abstract films, such as Norman McLaren's, a degree of popular appeal are absent. Brakhage's shapes are hard to limn; the imagery goes by very quickly; there's no obvious "compositional logic"; the rhythms are unpredictable; there's little repetition. Most important, his films represent ongoing struggles for both maker and viewer. Adrift in a sea of color and light, the viewer is forced to navigate a groundless, boundless wilderness that may at first seem to consist of the raw meat of seeing — one of the films on this program is titled The Lion and the Zebra Make God's Raw Jewels.

Brakhage is not being ornery: these absences evolved from the ethos underlying his first book. But at times that ethos has been misunderstood: his assertion that assigning names to things limits our ability to see them has often been mistaken as claiming that his films incorporate a way of seeing akin to an infant's — yet a few paragraphs later he acknowledges the impossibility of returning to childhood, "not even in imagination." And his films of the 60s and early 70s were dense with metaphoric associations and suggestions of narrative. Indeed, these somewhat representational films are usually characterized by a tension between the multiple associations of their recognizable objects, associations carefully shaped through editing, and an approach that emphasizes graphic and textural qualities or pure light. Most of Brakhage's films before 1974 — the year he made his first long abstract work, The Text of Light — can be said to have an identical underlying "plot": the people and objects in the world represent light and energy bound up in specific material forms, and the filmmaker's task is to capture the auras of light that might suggest their original divine spark — a gnostic view that also recalls the current scientific version of the origins of the universe.

In The Text of Light — a film approximately 70 minutes long — almost all the images are very close views of refractions in a crystal ashtray. But however nonrepresentational the work may seem, the filmmaker — who's long hated the word "abstract" — argues that its images tell a kind of creation story involving volcanoes, mountains, and rivers. In the years since 1974, though he's made superb films that applied his technique to recognizable subjects, most of Brakhage's greatest works have pushed abstraction to hitherto unimagined extremes, challenging all our usual modes of perception. What Brakhage's later films implicitly attack is no longer just the naming of things but all forms of learned seeing and thinking, everything predictable, every immediately graspable image, and all the conventional symmetries and repetitions of most past art, even abstract art.

Yet each work has its own tone, and some titles invite real-world associations. On this program, the fluttering waves of color in Earth Song of the Cricket do suggest cricket wings, though the transparent colors seem even more variegated and detailed. Cricket Requiem is slower and has a black rather than mostly white ground; it also develops a bit less dynamically, in more of a monotone — like a dirge. Both films include painted fragments full of sensuous detail that last only a fraction of a second: these compositions don't "invite us in," the way those in mainstream films often do, in part because 1/12th or 1/24th of a second is hardly enough time for a visit. These films seem to be made at the pace of neurons firing, and they're meant to be experienced that way.

The best avant-garde films often oppose both mainstream cultural values and what's expected in cinema. And a few Brakhage films began as responses to mainstream culture: the impetus behind The Lion and the Zebra Make God's Raw Jewels, Brakhage told me, was his unhappiness with how very often, when he sat down to dinner, his two young boys wanted to watch "those horrible animals-eating-animals programs on the Discovery channel," in which "the British narrator's voice says it doesn't really hurt them as you watch them get eaten alive." He also felt, however, that "God made these creatures and they do this," and he tried to envision their torn flesh in the film as "raw jewels." Ever skeptical about titles, Brakhage also says, "There are many other things that The Lion and the Zebra really could be that are limited by that title." But I found it easy to imagine the film's painted images as raw flesh: reds and browns predominate, the shapes look stained and partially liquid, and they seem ripped rather than complete in themselves. In the transitions between shapes, one form often seems to be tearing itself away from the last. As in most of these films, Brakhage also superimposes shapes on other shapes, which can still be seen; near the end of the film, more and more of the frame is colored in. Along with this greater density comes a slight steadying of the rhythm, and suddenly it seems as if these flesh shapes were being recombined in almost architectural sequences to build something larger than themselves. On a "plot" level, Brakhage seems to depict nature's cycles, the way that fragments of plants and flesh become new plants and new flesh. All these films move away from showing pictures of things in order to capture the processes that undergird the world — or that underlie thought itself.

The longest film on the program is called simply ... . For the sake of programmers and catalogers, however, Brakhage says it's permissible to title the work ... (ellipses) or Ellipses. Though this is now a five-part feature-length film, only the first reel (the only 1998 work on the program) is being screened Friday. Brakhage usually allows films in series to be shown separately, but I've found that such films often have more meaning when seen with the rest of their group. This reel is nevertheless stunning in itself: its stark lines and shapes cut into the emptiness around them, suggesting the evolving glyphs of an unknown language. Visually sparser than the other films on this program, it was made entirely without paint. After successful surgery for bladder cancer, Brakhage started to feel angered that his past use of dyes made with coal tar had probably caused the disease. He didn't want those emotions to interfere with the creative process, so he abjured all use of paint. (The later works were made with nontoxic dyes.) Starting with black film made from color emulsion, he scratched it to varying degrees of depth, revealing some color at the edge of his scratches, and used colored light in the printing to tint the film.

The lushest and most fully realized of these six works are Coupling and Persian Series. In Coupling a dense, ever changing yet interconnected field of neuronlike shapes in tan and green presents the eye with a monumental tangle. Even more than in the other five films, here it's hard to separate Brakhage's marks from the neutral ground; the field can't be reduced to any of its constituent parts.

By Brakhage's account, Coupling was one of his most complex and time-consuming projects, requiring six months to complete. Early in his work on this film, he painted shapes inspired by live nude models of both genders on the celluloid, hoping "to get a sense of the organs inside, not just liver, bladder, and heart but connective tissue — to suggest both microscopic and larger organs during coupling." But he wasn't thinking only of sex: "I wanted Coupling to include the complexities of connective tissue during hand shaking or throwing an arm around a shoulder." The film's richness results in part from Brakhage's use of multiple layering, achieved during the printing process in two ways: by normal superimposition, which enhances the light areas of the image, and by bipacking, which shines light through two layers at once so that the dark areas in both become even darker. This sense of light as both additive and subtractive creates part of the film's mystery: some of the shapes shine outward while others seem blockages or masks; this juxtaposition further dematerializes the shapes. Various layers of both types are combined, sometimes merging and sometimes retaining their separate identities, giving the impression of polyphonic music. The film's sense of multiplicity doesn't so much suggest an orgy, however, as an utterly diffused consciousness, not focused on a single body or moment but seeking to embrace the universe.

Persian Series is the latest of several series inspired by the origins of written language that Brakhage has made over the last two decades; among the others are Arabics, Egyptians, and Babylonians. Persian Series 1-5 is on view here, but a sixth in the series is also completed. "I'm working with the unnamable shapes that arise from human thinking, and how then those take shape as glyphs or script like the alphabet and numbers and symbols and pictures. They're imaginary series, but it's a thoughtful imagination, not just anything goes." For Persians he studied reproductions of Persian miniature paintings, their decorative borders, Persian rugs, and the culture's calligraphy. And certainly the lush color schemes of Persian miniatures are reflected in these densely layered films. At one point in the second, a series of zooms in suddenly becomes a massive zoom out, creating the effect of a precipitous balloon ascent from the landscapelike shapes we've been seeing. Yet the "aerial" view that materializes is not fundamentally different from the "closer" images: on any scale, the imagery remains a skein of interconnected organic shapes worthy of nature's fractals.

What's extraordinary about Persian Series, however, is the way it achieves an even greater dislocating and redefining effect than the other recent films, with layering almost as complex as in Coupling and shapes and colors that are even richer. The eye is typically possessive: it wants to plumb the image, know it, catalog what it has to offer, and file it away. This is how we remember faces, landscapes, objects, and it's this kind of seeing Brakhage disrupts so profoundly. It's not simply that the viewer can't name what he sees — he can't fully see it, and in that sense can never fully understand or own it. By mixing shapes related to one another with a form that abjures predictability and repetition, by mixing order and apparent randomness (surely Brakhage can't control every tiny splotch), by using layers of images that prevent the eye from locking in to any one, he shifts the viewer from comprehending solid objects in the "real" world to a state of profound self-questioning: his real subjects are not specific objects or ideas but the kind of raw neural processes that underlie all sight and thought.

Brakhage's transitory, fragmentary shapes, which the eye almost frantically seeks to grasp, remind the viewer of the value of every fraction of a second, every instant of time. His films make me feel alive precisely because they're so demanding, constantly asking us to see in unaccustomed ways and veering in unpredictable directions. Their imaginary topographies are a world away from Renaissance perspective, with its notion of mappable "real estate," to use Brakhage's words. With their imagined shifts in scale, these films are truly beyond measure; viewing these works, it's as if one's consciousness were being pulled apart. Indeed, Brakhage once said that he uses film to discover what he does not know.

Sadly, the films on this program may mark the end of a certain kind of filmmaking for Brakhage. The lab he's used most of his life, Western Cine in suburban Denver, has experienced the same decline in business as most film labs and has been forced to dismiss Sam Bush — the person who's printed Brakhage's films for decades and has sometimes been credited as a collaborator. It's also planning to sell the elaborate optical printer used for most of these films. (There is a less sophisticated optical printer available to Brakhage at the University of Colorado at Boulder, where he teaches.) But, then, Brakhage once said that if the manufacture of motion-picture film ever ceased, he'd make scratchings on rocks on the beach and line them up like dominoes to make a primitive flip book when they fell. His work is evidence of how deeply cinema and the mind can be connected, interweaving thought and image, reflecting the perhaps naive utopianism of an earlier era: see a film, change your consciousness, make a better world.