Try this: 
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

[download]

For each line that begins with an upper case letter it pushes a new array reference onto @matrix, and for all other lines it simply pushes the data onto the last array in @matrix.

If you have to deal more with Fortran output, take a look at Fortran::Format.

In reply to Re: Read fortran list output by moritz
in thread Read fortran list output by madd

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