wages :
I am confused by your title. Are you asking how to clean a Windows machine using a Linux machine?
Either way, if you suspect that your machine has a rootkit then your ONLY sensible option is to completely reinstall the OS from known secure media. You will most likely not be able to detect or even remove a rootkit. Your machine is irreparably compromised and I hope that you have the data backed up.
you have got to be joking.. out of 100s of virus machines , malware, root kits i clean on a weekly basis i have had only a hand full that have been so far gone they could not be repaired. A root kit is not the end of the world to your machine " tho im finding it hard to believe your able to detect and know for sure you have a root kit and not have the ability to just remove it manually in the first place "
honestly i use linux as my main pc for home computers but when it comes to cleaning up a windows machine its so much faster to do it by hand most of the time but it can be nice to use for just 1 i.e. trinity rescue kit or something "set it and forget it" but its long.. very long to scan multiple times.
If you have an xp machine then just "if you can stay in the gui" clean all the temp files out of your drive use ccleaner or something.. then run "combofix.exe" (wont work on win7 only vista and xp) after that's completed run malware bytes and that honestly should take care of 90% of your work except the root kit.. use reveller etc etc find out which kit it is and look up manual removal steps.. honestly if you know you have a root kit you should have the name and things to search for already... if you only think its a root kit, try the first 3 scanners and see if your truly clean.