You will get better answers if you provide us with more context around your problem. After reading your question, my spidey-sense is going off. Forgive me for making a wild guess, but are you a Perl novice tasked with maintaining a script originally written by an experienced Perl programmer?

Is the my $file = shift; part of a subroutine? If so, show us the complete subroutine and where it is being called. Do you understand how the unwanted "." got there in the first place? Are you certain it needs to be removed? Instead of removing it in the subroutine, does it make more sense to ensure it isn't passed to the subroutine in the first place?