my (@array1, @array2);
open( F1, "datei1") or die $!;
open( F2, "datei2") or die $!;
while ( 1 )
{
$daten1 = <F1>; 
last if not defined $daten1;
push( @daten1, $daten1 );

$daten2 = <F2>;
push( @daten2, $daten2 );
}
close (F1) or die $!;
close(F2) or die $!;

subprogramm( \@daten1, \@daten2 );

open FILE1, $file1 or die $!;
open FILE2, $file2 or die $!;

while (defined(my $line1 = <FILE1>) and defined(my $line2 = <FILE2>)) {
    doAnything($line1, $line2);
}

23.343434  0.0343   0.2344   #Beginn Datensatz 1
23.354553  0.1234   0.3443
.
ca. 20000 Zeilen
.
.
24.343434   0.3434   0.3434   #Ende Datensatz 1


23.343434  0.0343   0.2344   #Beginn Datensatz 2
23.354553  0.1234   0.3443
.
ca. 20000 Zeilen
.
.
24.343434   0.3434   0.3434   #Ende Datensatz 2


usw.

#!/usr/bin/perl

use strict;
use warnings;

my $file_1 = '/pfad/zur/datei.txt';
my $file_2 = '/pfad/zur/datei.dat';

{
   local $/ = "\n\n";
   open(my $fh_1,'<',$file_1) or die $!;
   open(my $fh_2,'<',$file_2) or die $!;
   while(defined(my $entry = <$fh_1>) and defined(my $entry_2 = <$fh_2>)){
      tu_was($entry,$entry_2);
   }
   close $fh_1;
   close $fh_2;
}