Reconfigure a nerd's app — that's rough! (9)
I believe the answer is:
sandpaper
'rough' is the definition.
(thesaurus)
'reconfigure a nerd's app' is the wordplay.
'reconfigure' is an anagram indicator (I've seen 'reconfigured' mean this).
'a'+'nerds'+'app'='anerdsapp'
'anerdsapp' is an anagram of 'SANDPAPER'.
'that's' is the link.
(Other definitions for sandpaper that I've seen before include "Abrasive substance" , "Spared pan for the stuff used to prepare surfaces" , "Material used for smoothing" , "Smooth" , "Make smoother" .)