External Harddrive bug

I recently reformatted my computer and used a Western Digital external harddrive to store my stuff while I did it. When I reinstalled CCleaner it froze and ctrl/alt/del declared it to be 'not responding'.

I was distressed, but I noticed that the external harddrive was audibly operating when I tried to run CCleaner, so I unplugged it and the cleaning went off without a hitch.

Rather than unhooking my external everytime I want to clean, is there a better way?

Please keep in mind that I'm not as computer savvy as this post makes me sound.