If the transmission and clutch are working properly...its probably not either of those.
Lots of things under the hood can rattle but some things I would check are: Engine mounts, sway bar end links (I would recommend Massive's as a replacement), sway bar bushings (under the car on top of the subframe).
More detail about the noise may be able to help pin-point it better.
2012 Fusion SE 3.0L V6
'86 XR4Ti ; 2.3L Turbo, 15psi
1988 F150 Custom
'07 ST ; formally bewst'd - R.I.P
D23 Crew: #07