You could certainly read the file in using binmode but, as wol noted, you do loose end-of-line handling. Depending on what is happening with your file before the parsing stage, you may want to try preprocessing it before the parse step.
Assuming that your file should only have word characters in it (as defined by \w = [a-zA-Z0-9_]), you could try this one-liner
perl -i.orig -p -e "s/\W+/?/g;" <yourfile>
This will rename the original file <yourfile>.orig and change every occurance of a non-word character to a question mark. I am assuming here that you want to retain the relative location of the offending byte. If you don't, simply write s/\W+// instead of s/\W+/?/.
If you wanted to write the output to STDOUT say before passing the data to another process you can omit the -i.orig flag
Of course, you could do it with sed or gawk but this is PerlMonks ;o).
use strict; use warnings; use diagnostics;