good idea to put in the year and model of your car.  New MINI or classic?  pedal is not connected mechanically to engine  so a vibration might be anything from a bad motor mount to a loose clutch pedal and likely something else.

I have just installed my new clutch and main seal. I also changed the slave cylinder and had a LOT of trouble bleeding it. I think it's ok now and the pedal has good resistance all the way, but I have a strange vibration in the pedal when engine is on and I'm resting my foot on the clutch, almost like a metallic clicking. Will this go away or is something wrong with the throd bearing or something else maybe? I replaced the clutch disc, throd bearing and pressure plate.