Disguises are used in both a literal and symbolic sense throughout The Scarlet Pimpernel.
By and large, disguise is used extensively by Sir Percy in order to do his work as the Scarlet Pimpernel. He disguises himself in all sorts of ways to rescue French aristocrats from being executed by the revolutionaries. He usually picks the most unexpected roles to play: an elderly woman transporting a "son" with the plague is the most famous. However, such theatrical disguises are not the only sort adopted by Percy—and he is not the only character to disguise himself.
In society, both Percy and his wife, Marguerite, adopt "disguises" to mask their true feelings. Percy pretends to be an insipid fop so that no one would ever suspect him to be the dashing, clever Pimpernel. He also acts coolly towards his wife, despite being madly in love with her, because he believes she betrayed the Marquis de St. Cyr and his family to the revolutionaries due to the former having her brother beaten. While she did seek vengeance, she did not intend for the family to be guillotined, but Percy does not understand this. For her part, Marguerite also acts as though nothing is wrong with the marriage in public, but behind the scenes, she is disgusted with Percy's foppish ways, unaware it is a facade. (That Marguerite is also an actress is a tie-in to the disguise motif running through the story.)
At the end of the novel, all disguises are taken off by both parties. Percy and Marguerite rekindle their love and see through the lies and facades which previously estranged them.