There is an 1:1 ratio in the quality of soundcards. the more money you spend the more quality you'll get.
In my recording software there is a built-in dehisser filter. I guess some free vst should wait for you in the www.
Also try this:
detach all audio sources (mostly line-in)
press record in your software
if you get the noise again then the reason is the soundcard. Otherwise check preamp noise when you record with a microphone.

What are you recording from, is it audio midi, preamp etc
Explain your complete set-up