“People just don’t surrender to my movies, ever,” says director Alan Rudolph, on the phone from his home on an island near Seattle. “They keep waiting for a regular movie to break out, and when it doesn’t they just hate them! I don’t know any other way.”

For almost half a century now, Alan Rudolph has been making movies that have connected more with individuals than with crowds or a large critical majority (from Mrs Parker and the Vicious Circle with Jennifer Jason Leigh to Afterglow with Julie Christie). By his own account he’s never really been any part of the conventional film industry – and he hasn’t made a movie since 2002. “If I could use a metaphor,” he says of his recent hiatus, “I was promised a few rides and they didn’t show up, so I decided to walk. I just got so enamored of the scenery and the pace that I just kept on walking. I started painting about 10 years ago and that kinda consumed my life. I enjoyed it a lot, the creative itch was being scratched, I could finance it on my own, and I didn’t have to talk to anyone – those were high priorities at the time.”

But now he’s back. His new movie, Ray Meets Helen, a typically wry and romantic, fable-like confection starring longtime collaborator Keith Carradine and a surprisingly affecting Sondra Locke. Ray’s a broken-down boxer who’s tracking money lost from an armored truck, while the meek and lonely Helen assumes the identity of a dead woman. It feels almost like a comeback – if Alan Rudolph were foolish enough to believe in comebacks. Sometimes he’s not even sure there was a first time around.

“I thought this was about as starting-over as you can get. It was so low-budget that the money was actually gettable. I wanted to present a fable, the real world as it presents itself to us. Just sand off all the curlicues, and boil it down to basic situations and basic actors, and it didn’t matter if there was a resemblance between the characters and real people or the real world. I wasn’t going for that. I wanted it to be a sort of unreal reality from the beginning.”

In its wispy romanticism, Ray Meet Helen harks back to earlier dazed and bemused, consciously artificial Rudolph movies like Choose Me and Afterglow, but with his usual subtexts of isolation and emptiness bubbling below. He freely admits that, like most of his movies, it isn’t for everyone – and it may not be for anyone.

“I have no common place in contemporary film, not then, not now,” he admits of his four decades of work. “I never got the Hollywood deal, I’ve lived up here for over 30 years – literally and figuratively on an island – I never went to film school, I never went to big Hollywood parties, I never had a PR person, which is probably why I used to call myself Captain Autonomous-Anonymous. I was never in favor with any group, be it audiences or critics or the financing system. They and I didn’t hear the same tune from the beginning. I barely had an agent half my career, and for me to go out begging for money at this age – some old guy no one’s ever heard of, and if they have, they don’t like his movies anyway! – I find it ridiculous.”

But this most outside of all outsider directors actually grew up in Hollywood, in a movie-making family, a happy hostage of the Dream Factory.

“You can’t trust my connections to reality because I was born into fantasy,” says Rudolph. “My father was connected to the movies every day of his life. He was brought out from Cleveland as a kid and his mother took him around until he got a job as an actor in a Mary Pickford silent movie. During the Depression he was an extra. Then he became Cecil B DeMille’s assistant director, and when television came along he became a TV director and did a whole lot of Brady Bunch episodes, to name just one job among many. When I was a kid, I’d be on all these soundstages with him at Paramount. You walk in to these giant cold, cavernous stages – I’ve always said I thought it was the padded walls that made me feel at home – and you see this blinding light somewhere on the horizon in this giant room – all the quiet, all the focus, all the artifice in the room – it’s suddenly the only reality.”

And he was mentored in film-making by no less a master than Robert Altman, for whom he worked as assistant director on The Long Goodbye and Nashville. “Bob and I overlapped but we were obviously different. He influenced my film life and my real life, and I’m proud of that. But I’m not Altman. He always had a big picture. This guy was flying B-24s in the second world war when he was 19 years old. I mean, nothing scared this guy. He was larger than life at every level – he was a wizard, an alchemist, quite brilliant in a non-academic way, and his instincts were … well, there was a dark wisdom to everything that Bob did. But working with Altman, especially after I saw McCabe and Mrs Miller for the first time, I saw that his working process was so much bigger, higher, wider, smarter – I mean, exponentially far ahead of my own way of thinking at that point.”

In his chosen corner, Rudolph has knocked out slightly misshapen, often “unabashedly romantic” (his phrase) pictures that have a lovely handmade feel to them, even if they don’t always quite work, which he admits can happen. His first movie, Welcome To LA in 1976, used collaborators he’d met on Nashville (Carradine, composer Richard Baskin) and a parallel musical milieu, and was immediately abandoned: “United Artists took one look and turned it down flat!” His second Remember My Name, took on the 1940s noir staple of the vindictive femme fatale, but was dropped on sight by Paramount (A pity: I think it’s half a masterpiece, with an insanely reckless and brave performance from Geraldine Chaplin.) Ever after, Rudolph’s always haphazard distribution was achieved “Willy Loman-and-a-suitcase-style. Here I was thinking I had done my best work, and it was treated with disdain.”

“Two movies, two orphans,” as Rudolph says, and the pattern for his career was set. Since then his movies have ranged from minor hits like 1984’s Choose Me, also starring Carradine, and genre-tweaking noir-romance Trouble in Mind (which found a new Alphaville in Seattle), to literary comedies about art and commerce like The Moderns, set among the expatriate Lost Generation in 1920s Paris, and Mrs Parker and the Vicious Circle, about the sexual and social roundelays of the Algonquin Round Table. There have been oddities like the screwball noir of Trixie and the more commercially minded thriller Mortal Thoughts, with Demi Moore and Bruce Willis.

Like his mentor Altman, Rudolph has used genre staples and archetypes for his own ends. Carradine in Ray Meets Helen is Burt Lancaster from The Killers dropped into an oddball romantic fable, while Geraldine Chaplin in Remember My Name is a psychotic Barbara Stanwyck in sunlit noir, and Jennifer Jason Leigh’s Dorothy Parker rattles off daffy quips and bon mots faster any movie character since Rosalind Russell’s Hildy Johnson in The Front Page.

With a half-century of work under his belt, often made under the most impossible circumstances, Rudolph feels he has the right to scorn the “independent movie” as we’ve understood it since the rise of Miramax.

“I have to laugh at the evolution of the term “independent film-making” – when I started that didn’t exist as a label. What I was doing with Altman was almost more independent than anybody then or since. I used to say: “Give me a little budget and I’ll be happy working over here in my little corner. But … don’t you ever touch my fucking corner!”

• The Quad cinema in New York is hosting an Alan Rudolph retrospective until 10 May and Ray and Helen will be released in the US on 4 May