328867 Viruses on my server

Hi there am having some problems with my sites there has been some viruses or small codes which are ditarbing my sites and need to be removed . I have a deticated server and have 2 domains on it but there are about 4 subdomains infected and need to remove infections and get them up and runing. Please beat low as I don't have a lot of buget for this but it needs a very close inspactions as the subdomains have diffrent scripts installed.