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#!perl

...
    $found = 0;
    @words = 0;
}

Applying pattern match (m//) to @array will act on scalar(@array) at C
+:\blah\vertailu2.pl line 24.
Global symbol "$fh" requires explicit package name at C:\blah\vertailu
+2.pl line 8.
Execution of C:\blah\vertailu2.pl aborted due to compilation errors.

    if ( @col2 =~ m/$words[$_](\d+)/ ) {
        $found++;
        @words++;
    }