First of all, do you know how exactly the virus got onto your pc? Did you open an email, or maybe use a crack for some program that you downloaded from the internet? Was this cracked program maybe the Internet Download Manager? If somehow the virus got executed within wine, it is very well possible that it did some harm, which will probably be only within your wine installation.
If the program that you are running is some suspicious file (e.g. if it is a crack downloaded from the internet) it is possible that this program is itself the virus you are talking about. As someone else already mentioned in the comments, there are alternatives for these programs, that don't require wine to run. For now, you should consider using those. Why did you use Internet Download Manager in the first place, does it provide any functions that other (free) download managers like JDownloader or gWget do not provide ?(I'm asking so that we can provide you with suggestions for linux alternatives that provide the same functionality)
You should also consider installing clamAV, which is a virus scanner for linux. It will allow you to scan your data partition, and remove any infected files. Otherwise, whenever you copy your data to another windows machine, you will risk infecting that machine as well! You can look into this question for more information on clamAV.