transfer function estimation

[Rudolf Widmer-Schnidrig]

Dear List,

to estimate the transfer function of a liner system I feed a well 
defined input signal into the system and record the output.

One way which I have followed so far is to FFT both the input and the 
output, divide output by input and feed
the resulting spectrum into invfreqs. This gives me the desired 
pole-zero representation of my system.

Question: can this be gotten without first FFTing the input and output?
What routines would I call?

I'd be glad to just get a sketch of the necessary steps.

                 sincerely,                 -Ruedi