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]