Unfortunately, although quite a few programs can remove various malware, they can not repair the damage such malware caused.
Simple spyware can usually be completely removed, and the system is not damaged. Other stuff like Trojans, more complex spyware, rootkits, and similar stuff, cause damage to the system. This damage remains even after removing what caused it.
In your particular situation I would run a
FULL scan with the free version of this;
Malwarebytes
and see what it says.
Then I would run a full scan with this;
SUPERAntiSpyware.com | Remove Malware | Remove Spyware - AntiMalware, AntiSpyware, AntiAdware!
and see what it says.
If both come up clean, then you can try to repair whatever damage the malware did to your system, although this is rarely successful, as it is difficult...impossible to find out what damage it did.
Once you have removed all the malware, it is usually best to reinstall a clean system. You should backup what you need
AFTER scanning it for malware.
Scan ALL partitions and drives!
Regards....Mike Connor