How about: 
my $rindex = rindex($imagename,'.');
$rindex    = length($imagename) if $rindex == -1;
substr($imagename,0,$rindex) =~ s/\W/_/g;

[download]
It will exclude the extension from the substitution.

Update: Fixed bug for filenames w/o extensions that end in a nonword char.

Update2: Thought I'd golf this one a bit: 

substr($file,0,rindex($file,'.')%length"a$file") =~ s/\W/_/g;

[download]
works correctly for $files such as "me~swimming.jpg", "J.R,ewing.jpg" and "abc;;;"

-Blake

In reply to Re3: Changing file names as they are uploaded by blakem
in thread Changing file names as they are uploaded by katgirl

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