way 1: (Doing it late)

foreach my $file (@files) {
    next if $file =~ m#/CVS/#;
    next if $file =~ m#~#;
    $file =~ s#^\./##;
    push(@noCvsDirs, $file);
}
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way 2: (Doing it early)

my $full_file = ($dir eq '.' ? $file : "$dir/$file");
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way 3: (Doing it early, the portable way!!)

use File::Spec ();

my $full_file = (
   File::Spec->canonpath(
      File::Spec->catfile($dir, $file)
   )
);
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* The \ in /\~/ can be removed: /~/

* m#/CVS/# is more readable than /\/CVS\//.

* m#/CVS/# and m#~# can actually be combined into m#/CVS/|~#.