Thank you sir, that was exactly what I needed. I attempted to incorporate what Graff said below, but quickly found that it what he said is above my level, at least at the moment. I still am quite new and learning things, so thank you so much for your suggestion and coding. I'll attach what I ended up with here in case you see something "bad" or whatever, I simply added what I wanted before it, and allowed a variable definition in the regex search. I understand what Graff was saying enough to catch that what I'm doing is a bad idea, but in time I'll learn better ways and make do with my limited knowledge for now. Thanks to you and graff both!
#!/usr/local/bin/perl -w
use strict;
use warnings;
print "Enter the output file you would like to analyze: ";
chomp (my $filename = <STDIN>);
print "Enter the isotope you want to extract (ex: Am-241): ";
chomp (my $iso= <STDIN>);
open(IN, "<", $filename) or die("Can't read the source:$!");
open(OUT, ">Comp_$filename");
select (OUT);
$/ = '0AVERAGE COMPOSITION IN PINS.';
while (<IN>) {
next if ! /$iso/;
chomp;
print "$/$_";
}