Hi, Try this,

while(<DATA>){
s/\]([ATCG]*)\[/'N' x length($1)/e;
print $_;

}
__DATA__
TG[CCC]CC[TTT]
TG[CCC][TTT]
TG[CCAAATTT]

Respective Output is:

TG[CCCNNTTT]
TG[CCCTTT]
TG[CCAAATTT]
[download]

Updated: monkfan, Try below code for your second question.

while(<DATA>){
s/\]([ATCG]*)\[/my $a = $1; $a =~ s![^C]+!'N' x length($1)!e; $a/e;
print $_;
}
__DATA__
TG[CCC]CC[TTT]

Respective Output is:
TG[CCCCCTTT]
[download]