How can I remove rotten nails? Is there any special tools I can use?

Answer 1

i take it you meen that the heads are gone?
nail nippers work well, kind of like a pliers with 2 clamps for teeth. also if ya dont care about the wood, use a catspaw and drive it into the wood with a hammer at an angle to the nail and pry it out.
you could also try drilling it out with a slightly bigger drillbit

Answer 2

You need an old-fashioned nail-puller like a Cooper Group 56 Nail Puller. Even gets out deep embedded nails.

Answer 3

Why not countersink them and fill in the hole with wood putty.