Recapping my understanding of your problem to see if I've it it right:

If you put names into a file one per line then your program can be used to tell you that a line contains a specific name and you can print just that name by printing the line from the file. However if you use a file containing lists of names then you get the whole line printed and that is not what you want.

However I suggest that isn't all your problem because you could just:

...
    if ($name =~ /Cobray/) {
        print "Cobray\n";
    }
...
[download]

So what is the bigger picture? Where is your real problem?