The third parameter should be a length, not a position.

substr($line, $pos1, $pos2-$pos1+1) = cleanse(substr($line, $pos1, $po
+s2-$pos1+1));
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Update:Here is some sample code, simplified in its input and output. The "local *tmp" trick by Fletch would also work, but I found it wouldn't pass strict without a "use vars qw($tmp);", so I went back to the simpler temporary variable idea.

use strict;
my @pos = (0,5,15,20);

while(my $line = <>) {
   my $i = $#pos;
   while ($i >= 1) {
       my $pos1 = $pos[$i - 1];
       my $pos2 = $pos[$i];
       my $len = $pos2 - $pos1 + 1;
       my $part = substr( $line, $pos1, $len );
       $part =~ y/'//d;
       $part =~ y/a-zA-Z0-9\n\|-/ /c;
       substr( $line, $pos1, $len ) = $part;
       $i -= 2;
   } # end while $i
   print $line;
} # end while
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