Transfer function estimation from logarithmic sweep frequency response data I have complex frequency response data (of an analog system) in the range of 100 Hz to 100 GHz, and it is sampled in frequency with logarithmic spacing. I would like to be able to turn this into a filter in MATLAB such that I can multiply it with the fft of time-domain signal.

I'm not seeing a good match when using invfreqs.  What is the best way to do this?
Use FDLS (Frequency Domain Least Squares) to create a model of your measured frequency response. Use the frequency response of that model, evaluated at the FFT bin frequencies, as your filter. 

Alternate: if a low-order IIR (or perhaps even FIR) model provides a good-enough fit, then use the model as your filter for direct time-domain convolution.