The code you posted didn't generate the output you posted because there were a bazillion syntax errors. The following code fixes the syntax errors and possibly generates the result you want. The key issue was assigning your results to $Delta which is a different variable to the array @Delta.

#!/usr/bin/perl
use strict;
use warnings;

my @Molecule_01 = (
    ['C', 0.2565522,  -1.5308230, 0.0000000],
    ['C', -0.8038556, -0.7047550, 0.0000000],
    ['C', -0.8519687, 0.7637319,  0.0000000],
    ['C', 0.3236482,  1.5968480,  0.0000000],
    );
my @Molecule_02 = (
    ['C', 0.3916152,  -1.5774692, 0.0000000],
    ['C', -0.8180007, -0.7937790, 0.0000000],
    ['C', -0.8314989, 0.6754852,  0.0000000],
    ['C', 0.1934963,  1.5451038,  0.0000000],
    );
my @Delta;

for my $i (0 .. $#Molecule_01) {
    my $row = $Molecule_01[$i];
    my @rowResults;
    
    push @rowResults, $Molecule_01[$i][0];
    
    for my $j (1 .. $#{$row}) {
        push @rowResults, $Molecule_01[$i][$j] - $Molecule_02[$i][$j];
    }
    
    push @Delta, \@rowResults;
}

print "@$_\n" for @Delta;
[download]

Prints:

C -0.135063 0.0466461999999999 0
C 0.0141451 0.089024 0
C -0.0204698 0.0882467 0
C 0.1301519 0.0517441999999999 0
[download]