Low level noise causing sub flutter

Question

I have an 02 alero. I have installed vega subs and an amp. I have managed to get power and tunes but when the radio is at zero the subs have low level engine noise and the subs sit there and flutter. Increasing the volume drowns it out but increasing the bass boost just causes the flutter to worsen.All cable have been changed and I have even tried a new amp in the event it was an internal ground problem but with no success.How do I get rid of the flutter and engine noise?