Taint::Util is a nice little module that provides the ability to test taintedness of a variable at runtime in a simple and sane way. It also allows you to explicitly taint or untaint. It could, therefore, be used to re-taint a variable that has had whitespace stripped with a regex. But you should remember that only captures are untainted. Simple substitutions aren't.

The core module Scalar::Util also has a tainted function that can be used to test taintedness, but it doesn't provide functions to explicitly manipulate the state.

My suggestion, however, is to pass your inputs through "the Prussian stance" style of sanitization before you even deal with cosmetic cleanup (stripping whitespace). If the very first thing you do to your data is to retrieve the safe portions you want to work with, then the infiltration of tainted data through the rest of the program is minimized. It's far easier to sanitize close to the source of input than later on after the input may have been transformed and passed around to various other components of the application.

Test::Taint is also worth mentioning as it helps your test suite to test assumptions about taintedness.