It sounds like you need to simply rename the files. If this is the case, then a simple bash script can easily do this. First thing to do is backup the files, because you don't want to practice shell scripting on your only copy of the files (duh...).
This should get you started. You can either make it into a shell script, or just run the commands from a commandline, since it is evidently a one-shot process.
for cncfile in *.nc; do echo mv $cncfile $( basename $cncfile ".nc" ).txt; done
for cncfile in *.ncs; do echo mv $cncfile $( basename $cncfile ".ncs" ).txt; done
Run the script/commandline, and when you are satisified that it will do the right thing, remove the 'echo' command, to have it actually perform the deed.
If the files need to be processed in some way, you will need to specify what changes need to be performed.