A scanner will only scan the strip, the rest is image processing and
decoding of the pattern.
If you scan at a high enough resolution, you can apply an affine
transformation without losing the detail needed for decoding. Finding the
best parameters for the affine transformation matrix seem to be an
optimization task for which many applications offer ready to use
components.
Perhaps patent 5200598 can help in constructing a software version:
http://www.pat2pdf.org/ (and type in the patent number).
I haven't searched, but there probably will be something you can find with
a Google search. If not, let us know what your particular scanning issue
is, maybe someone can assist on that specific issue.