Morgan Miller has coffee stains on the sleeve of his shirt, on his briefcase, and even on his most recent animated work, There’s Too Many of These Crows.

“Coffee stains don’t bother me,” he says. Not even a tiny drop in the middle of the screen. “I mean, the audience ultimately knows they are watching a drawing so you can only fool them so much,” he says.

At 39, Miller’s self-referential work has given him a solid place in the independent animation scene. There’s Too Many of These Crows, which plays as part of the “Mind F*ck Shorts” program at the Lower East Side Film Festival tonight, has enjoyed success this past year, winning best animated film at the Stockholm Animation and Experimental Film Festival, first prize at the ASIFA East Animation Festival and best short film runner-up at the 2016 Bushwick Film Festival.

Miller does much of his animating at Pratt, where he also teaches. There, in the “Pencil Test Room” room, well-worn plastic light boxes mounted into each desk provide backlighting for animators as they trace their characters from one paper to another. They’re noticeably crowded out of desk space by giant, state-of-the-art Apple monitors.

“These computers were not here last semester,” Miller says of the monitors, begrudgingly. “A lot of these young people like using these computers, but I feel like you lose the human element.”

The human element is a common theme in Miller’s drawings and stories, and the human at the heart of them is his recurring character Jeff Twiller.

Jeff is a house painter in his 30s, an aspiring filmmaker, and a part-time YouTube commentator. He lives in the grimy, fictional world of Slushing Brooks, a decrepit city overrun with bugs and filled with trash and worn-down buildings. Miller’s pencil smudges and wrinkled paper add to the overall dinginess of Jeff’s daily life. Jeff is overweight, shy, horny, awkward in front of the camera, curses too much, and speaks in a low stuttering voice when he holds forth about weaponry and recent genre films like Prometheus and Looper.

It’s easy to like Jeff; his naiveté and awkward musings make him engaging despite himself. “He’s sort of an alter ego,” says Miller of the character, whom he also voices. “He is sort of a satire of people I know. He’s a little bit like my father, too.”

Miller often fools himself into thinking Jeff is a real person. “You know, sometimes I’ll see a movie and I’ll think, ‘I have to show this to Jeff,’ and then I’ll think, ‘Oh, but Jeff doesn’t exist,’ and then that’s really depressing. Sometimes I really want Jeff to be my friend.”

Born in New York City, Miller grew up in Rockland County where he started drawing at an early age. His mother, a painter, would make books out of folded blank paper and staples, and five- and six-year-old Miller would fill them up with his drawings of cowboys and Indians attacking each other.

Miller finished his first animated film in high school, after he taught himself using a book by Yvonne Anderson. The stop-motion film, entitled “The Proletariat,” pits two students, made of cardboard cutouts, against a “fascist pig” hall monitor named Beef. During a self-declared “proletariat uprising,” they end up stabbing Beef in the eye with a pencil, and we see the pencil disturbingly pierce his cornea in slow motion.

“I was 17 at the time but I guess there was some political analysis,” Miller says, smiling in recollection. “I’m pretty passive about politics now.”

After high school, Miller attended the School of Visual Arts in New York City and later finished his BFA in film at the University of the Arts in Philadelphia. Upon graduating, he studied briefly in England for his master’s degree and then, finally, returned to his home state to an apartment in East Williamsburg.

In person, Miller is difficult to read. His humor is dry, delivered with a straight face and low voice. His Jeff Twiller shorts are often the key to understanding him. Some are awkward and abstract (in one, Jeff silently contemplates a horde of ants) while others are closer to the grotesque, mainstream humor of South Park or Beavis and Butthead. In “Vacuum Attraction,” one of Jeff’s earliest appearances, he gets turned on by the lead actress of a fictional sci-fi show and gets stuck in a vacuum cleaner while trying to perform a sexual act on himself. It’s up to his coke-snorting, foul-mouthed, construction-worker friend Randy to free him.

Over the course of 40-plus animated shorts starring Jeff, we learn that Jeff has a food addiction problem, and that his father is supposedly off working for the CIA. His mother drives around the house in an electric scooter, with a nasal cannula hanging from her nose. Still, Miller doesn’t see Jeff as a tragic figure: “He winds up in tragic situations but he has a real passion for things that he’s interested in.”

Randy and Jeff also serve as narrators of “Twillerama,” a feature-length film of animated shorts from other independent artists curated by Miller. Initially screened in Brooklyn at Legion Bar in 2014, Miller’s first Twillerama was hugely successful, prompting a nationwide tour in more than 20 theaters across the country. Miller went to only a few of the screenings outside of New York, however; he doesn’t like to travel much.

Though Miller finds something like friendship in Jeff and his three sidekicks (Randy, Rod, and the painfully shy Enis), he sometimes needs a break from voicing them and writing jokes for them. During one such break, he finally finished There’s Too Many of These Crows, a project he had been working on for over four years. After its first screening, the short film surged in popularity, and has since traveled to animation and film festivals all over the world.

The film is set in a vaguely European small town. Miller did extensive research to get the costumes and weaponry of the Edwardian era just right, but added anachronisms and elements from various cultures. “I wanted it to be Fairytaleish,” says Miller. “You’re not quite sure if it is France or it’s Germany or it’s Britain, but it’s western Europe. I feel like if you are using animation it has to have some kind of metaphoric or fantasy element.”

The film opens with a farmer shooting a couple of crows. Suddenly, a flock of birds retaliates and starts attacking the farmer, eventually lifting him into the sky and then descending on his wife. Things get more bloody from there.

“Aggressors and imperialists often think being more technologically advanced gives them the upper hand,” Miller observes. “It doesn’t always pan out that way.”

The film is still well entrenched in the festival circuit, and will be shown tonight as a 2K DCP with 5.1 surround sound at Landmark Sunshine Cinema.

Miller’s current project is entitled “Nouns and Adjectives” and continues the trend of films with no script or voice acting. It will eventually feature a collection of disjointed sequences of sounds and activities, like a dog baring its teeth and barking. “I sort of got the idea from my cat,” says Miller. “Sometimes I wonder what my cat’s thought process is if she doesn’t have language and she doesn’t have words attached to things.”

So far, Miller has drawn two sequences on graph paper, both of which feature images surrounded by ink splotches that move around erratically. (The splotches are a simulation of the migraines from which he suffers.) It’s uncertain when the film will be done; Miller doesn’t rush his work, so for now they lie around, collecting coffee stains.