I agree with kwaping, I would use tr/// for this solution.

#!/usr/bin/perl -w
use strict;

while (<DATA>) {
    chomp;
    tr/[]//d;
    $_ = join(" ",split " ", $_);
    print "$_\n";
}

__DATA__
[
 [ 0.039543323]
 [ 0.068993981]
 [ 0.086558227]
 [  0.12252527]
 [  0.14724698]
 [  0.16631099]
 [  0.18877556]
 [  0.20234162]
 [  0.18110326]
 [  0.13155017]
[  -4.0316574]
 [  -3.6178487]
 [  -3.1186917]
]
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