Usually virtualization software is safe, unless the one you're using happens to have a bug that can be exploited. You can join their support forums to check for any updates with regards to their security.
If your android emulator allows you to reset to default settings (i.e. perform a factory reset), then you can clear your current session and start a fresh one.
Also, assuming that your pc (Host) is completely isolated to the virtualized environment (guest) Android system, then you should be safe using the emulator software as well.