The first step is to understand how badly your system has been compromised. Often there may be a mix of issues.
Running an anti-virus software may provide some clues, as may the message you receive from your internet service provider. However if your system is compromised there is a possibility that the diagnosis you receive may also be compromised or misleading.
There are a range of web-based diagnostic applications that may also be worth checking.
In many cases, however, it may not be possible to successfully remove all malware and return the system to a known-safe and stable configuration.
You may need to consider backing up your critical data, reformat your hard-drive and re-install a fresh version of operating system and your software.
If you feel this is beyond your abilities, seek advice from the specialists: go to the professional help page.