You can disable warnings at the file/function/block level:

{
   no warnings 'substr';
   ... use substr here ...
}
[download]

In the above snippet, substr will then return the empty string ("") without giving a warning when the start position is beyond the end of the string.

Another way is to check the length of the string on which substr is called:

my $substr;
if (length($_) >= 4) {
   $substr = substr($_, 4, 3);
} else {
   $substr = '';
}
[download]

sub find_process {
   ...
   if (length($file) < $x) {
      warn("Skipping file $file\n");
      return;
   }
   ... substr($file, $x, ...) ...
   ...
}
[download]

sub find_process {
   no warnings 'substr';

   ...
   my $part = substr($file, $x, ...);
   if (not length $part) {
      warn("Skipping file $file\n");
      return;
   }
   ...
}
[download]