#!/usr/bin/perl
use warnings;
use strict;

my @arr2 = qw( mcs scr tsz unh );
my @arr1 = qw( spec.srn.1234 sepc.mcs.1234 );

for my $strfile (@arr1) {
    my @arr3 = split(/[.\n]/, $strfile);
    if (grep (/^$arr3[1]$/, @arr2)) {
        print "Entered in IF Loop\n";
    } else {
        print "Entered in ELSE Loop\n";
    }
}

__END__

Output:
Entered in ELSE Loop
Entered in IF Loop