I wasn't quite sure what you wanted but if I understand you rightly then this should help. From what I can tell, you want to grab anything A~~~stuff~A and remove it from the string and print out what you removed. This snippet will do that for you:

$sentence = " he PP
       study VB
       A~~~language~A NP
       and CC
       play VB
       A~~~game~A NP
       .";
$_ = $sentence;
while (m/(A~~~([^~]+)~A)/g) 
{  
    # debug print
    print $1 . "\t" . $2 . "\n";
    
    # Remove our match
    push @parts, $2;
    $_ =~ s/$1//g;
}

$sentence = $_;

# print the bits we took out
foreach (@parts)
{
    print $_ . "\n";
}

# print the new sentence
print $sentence . "\n";
[download]

Hope that helps - one problem you did have was with your original match of A~~~(.*)~A. This greediness would have caused you real problems :P

For example, if your sentence had been

 $sentence = "A~~~one~A and A~~~two~A";
 $sentence =~ m/A~~~(.*)~A/g;
 print $1;
[download]

Then you are going to get unexpected results. You can use the non greedy quantifier ? to help out here or you can change the regex syntax.

HTH :)