Thank you! This is what I was able to come up with:

use File::Find;
my $dir = Cwd::getcwd();
my $string = "//Kartex TrackFil skapad av Kartex 5.4\n&KTF 2.0,sweref 
+99 lat long,1\n";
open (MYFILE, '>>merged.ktf');
print MYFILE $string;
close (MYFILE);
find(\&wanted,$dir);
sub wanted {
    if ($_ != /\.ktf$/) {
        print "$File::Find::name\n";
        open (KTFDATA, "$File::Find::name") || die("Could not open fil
+e! $File::Find::name");
        my (@raw_data) = <KTFDATA>;
        splice @raw_data,0,2;
        close (KTFDATA);
        open (MYFILE, '>>merged.ktf');
        print MYFILE @raw_data;
        close (MYFILE);
    }
}
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