while (my $line = <F>)
{
    if ($line =~ /$_/)
    {
        ...
        last;    # breaking while loop
    }
    else
    {
        ...
        last;    # breaking while loop 
    }
}

##</code><code>##

open (F, "$dir/$filename") || die ("Could not open $filename");

foreach (@store)
{
    ...
    while ($line = <F>)
    {
        ...
    }
}

##</code><code>##

open(my $F, '<', "$dir/$filename) or die "Cannot open file '$dir/$filename' for reading: $!";

OUTER: while (my $line = <$F>)
{
    foreach my $string (@store)
    {
        if ($line =~ /\Q$string\E/)
        {
            ...
            next OUTER;
        }
    }
}

close $F or die "Cannot close file '$dir/$filename': $!";