#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @tables;

while (<DATA>){
    chomp;
    next if m/^\|/;
    if (m/^\[Wertetabelle\d\]/){
        # neue Tabelle anlegen
        push @tables, [];
    } elsif (m/^\[Zeile\]/) {
        # neue Zeile anlegen
        push @{$tables[-1]}, [];
    } else {
        # Daten reinschaufeln:
        push @{$tables[-1][-1]}, [split];
    }
}
print Dumper \@tables;


__DATA__
[Wertetabelle1]
|
[Zeile]
A1 3.227
A2 1.127
A3 -1.471
[Zeile]
B1 6.684
B2 1.054
...