A movie about a man that is driving a capsule inside another man's blood stream. He controls his face by changing it to another man.
Down-on-his-luck naval aviator Lt. Tuck Pendleton (Quaid) resigns his commission and volunteers for a secret miniaturization experiment. He is placed in a submersible pod, and both are shrunk to microscopic size. They are transferred into a syringe to be injected into a rabbit, but the lab is attacked by a rival organization led by scientist Dr. Margaret Canker (Fiona Lewis) planning to seize the experiment and steal their technology.
Experiment supervisor Ozzie Wexler (John Hora), knowing their intentions, escapes with the syringe. A chase ensues with one of Canker's henchman and leads to a nearby shopping mall. After being fatally shot and knowing he is about to die, he injects Tuck and the pod into an unsuspecting Jack Putter (Martin Short), a hypochondriac grocery store clerk who happens to be the first person he comes into contact with.
By contacting Tuck's estranged girlfriend Lydia Maxwell (Meg Ryan), who has had dealings with the Cowboy, they learn that the Cowboy plans to buy the computer chip from Scrimshaw. After knocking the Cowboy unconscious using the pod's equipment, Tuck controls the muscles of Jack's face to make it look like the Cowboy's, and with him posing as the Cowboy, they meet with Scrimshaw and steal the chip from him. However, as they're about to take possession of the chip, Jack's nervousness overrides the transformation of his face, exposing the scam.
Fantastic Voyage, which I answered with originally, is the inspiration for Innerspace (but doesn't include the face morphing).
Face Morph clip (low-qual):
This movie is called Innerspace (1987).
A hapless store clerk must foil criminals to save the life of the man who, miniaturized in a secret experiment, was accidentally injected into him.
At one point he changes the appearance of Martin Short to look like 'The Cowboy.'