Chris Walas, who had designed the creatures in Gremlins, was hired to handle the film's extensive special effects. Filming took place in Toronto in 1985–1986.
The producers also commissioned musician Bryan Ferry to record a song for the film for promotional purposes. The resulting track was entitled "Help Me". A music video was made for the song, and footage from the film was featured heavily in it.
Cronenberg admitted to liking the song, but felt that it was inappropriate to the film itself. Brooks and Cornfeld originally wanted to play the song over the closing credits, but after Cronenberg screened it for them they agreed with the director that it did not mesh with the movie.
As a result, the song is featured only briefly in the film, in the background during the scene where Brundle challenges Marky in the bar. "Help Me" quickly disappeared and became extremely rare, as it was not included on the film's soundtrack release.
It resurfaced in 1993 on the Roxy Music/Bryan Ferry compact disc Ultimate Collection. The design of Brundle's Telepods was inspired by the engine cylinder of Cronenberg's Ducati 450 Desmo.
Deleted/alternate scenes: After filming ended early in 1986, a rough cut of The Fly was shown to Fox executives, who were very impressed. A rough cut was then previewed at Toronto's Uptown Theatre in the Spring of that year.
Due to a strong audience reaction, the graphic and infamous "monkey-cat" sequence was cut from the film to make it easier for audiences to maintain sympathy for Brundle's character.
Another preview screening was subsequently held at the Fox lot in Los Angeles, and this version featured the "Butterfly Baby" coda. As before, the screening results dictated that the scene be cut.
As with most of David Cronenberg's movies, The Fly was tightly edited to maintain a strong pace and to downplay the gore. The final cut runs a brisk 95 minutes, and although very few full scenes were cut, many others were trimmed down.
The DVD and Blu-ray editions of the film feature both the shooting script and a great deal of deleted, extended and alternate footage which had never been seen before.
The most notable deleted/alternate scenes include:
Second Interview: A short scene that features Veronica Quaife conducting a videotaped interview with Seth Brundle (after his superhuman exercise as seen in the completed film), in which he mistakenly theorizes that being teleported has somehow improved him.
A slightly different version of this scene appears in The Fly II, which contains alternate takes and dialogue that do not appear in the workprint version of the scene as presented on the DVD.
Additionally, Geena Davis' dialogue is overdubbed by Saffron Henderson, who took over the role of Veronica in the sequel.
Monkey-Cat: A legendary and infamous sequence in which the desperate Brundle (in a transitional makeup stage which appears only in this scene), uses the Telepods to merge an alley cat and the surviving baboon together in an attempt to find a cure for his condition.
However, the resulting "monkey-cat" creature comes out of the receiving Telepod terribly deformed and in unendurable pain. The creature attacks Brundle, who ends up beating the two-headed creature to death with a metal pipe so as to end its misery.
The sequence goes on to show the disturbed Brundle scaling the wall of his lab up to the roof, only to feel a sharp pain in his left side (specifically, in the hernia-like bulge seen in the final cut of the film when Brundle first demonstrates his wall-crawling powers).
He accidentally slips off the roof, slides down the wall, lands on a metal awning, and watches as a small, fly-like leg emerges from his torso. Horrified by this new appendage, Brundle amputates it with his teeth.
Brundle's motivation for fusing the two animals together was intended to be somewhat ambiguous in the context of the sequence, which featured a "test run" for Brundle's fusion "cure" seen at the end of the movie.
Thematically, the point of the scene was that Brundle was trying to find some kind of cure for his rapidly deteriorating condition, but was clearly losing his sanity at the same time.
The end of the sequence also revealed exactly what the hernia-like bulge on Brundle's torso was, as well as revealing the final fate of the second baboon, story points that are both left unresolved in the final cut.
As noted, this sequence was included in the rough cut shown at the Toronto preview screening. The audience had a strong reaction, with at least one person allegedly throwing up.
The general consensus from the preview audience was that Brundle was being cruel to the animals (and thus the scene played as being gratuitous, which was not the filmmakers' intent), and, as a result, they lost sympathy for him for the duration of the film.
The scene was cut, and remained lost for nearly 20 years. For the 2005 DVD, the scene was restored from the original negative (which was editorially conformed to the workprint version), with tracked-in sound effects and music taken from the completed film.
After amputating the insect leg, the script additionally called for Brundle to encounter a homeless woman in the alley, upon whose face he would vomit and subsequently consume.
However, this segment was written out of the movie before filming, even though an actress had already been hired to play the baglady. The scripted sequence appears on the DVD.