use strict;
use warnings;
use Data::Dumper;
my @matrix;

while (<DATA>){
    chomp;
    if (m/^[A-Z]/){
        push @matrix, [$_];
    } else {
        push @{$matrix[-1]}, $_;
    }
}
print Dumper \@matrix;

__DATA__
C
 -2.3242E-003
 1.32423
 0.34243E+002

..etc...

 -3.23134
H
 more numbers