It would help if you said which simulator you're using.

If spectre, all the noise analyses will compute noise figure if the input source is specified as a port, and you tell the noise analysis that the source is the input... (you normally want to specify the output as a probe, and probe the load port or resistor, to ensure that the noise from the load is excluded from the measurement).

The fact that you said ".noise" probably means you're not using spectre though...

Regards,

Andrew.