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Industrial Light & Magic (ILM), supervised by Stefen Fangmeier, created the film's 505 visual effects-shots. The filmmakers used as few digital effects as possible, though the train and smoke for the railroad crossing scene was entirely created using computer animation. ILM also used color grading techniques for the Lake Lachrymose scene, which required complete animation for the leeches. The digital animators studied footage of the 2003 Atlantic hurricane season to accurately depict Hurricane Herman, which was ILM's most ambitious use of computer-generated imagery (CGI) for the film.

Nexus Productions designed the opening "Littlest Elf" animated sequence by modeling it after stop motion animation and completing it with computer animation. The snakes at Uncle Monty's house were a combination of real snakes and animatronics. The animatronics, primarily the Incredibly Deadly Viper, were used as reference models that ILM later enhanced using CGI.

Because working with infants was sometimes risky in producing a film, four scenes involving Sunny Baudelaire required CGI with motion capture technology. Among these are the shot of Sunny hanging on to a table by her teeth, catching a spindle with her mouth and the scene where she is entangled with the Incredibly Deadly Viper. Animation supervisor Colin Brady used his baby daughter for motion capture recording. A remote controlled animatronic of Sunny was also designed by Kevin Yagher.