Here's another option that will append a "_" to the end of the three-character elements:

use strict;
use warnings;

while (<>) {
    s/\A...\K\Z/_/;
    print;
}
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Usage: perl script.pl inFile [>outFile]

The last, optional parameter directs output to a file.

The substitution attempts to match an element that has only three characters, and the \K notation forces the substitution to Keep those three characters, and then adds the "_" to the end of those.

Hope this helps!