Is there any utility in ferret which can do digital filtering of time series using FFT
I'm no expert in filtering, but I think there are FFT routines in Ferret. You Fourier-transform your timeseries, mask out (or weaken) some Fourier components, and inverse-transform it. You'll find documentations on Ferret's FFT routines on the website.
Having said that, you can often filter timeseries without going to the Fourier space. Typical high-, low-, and band-pass filters are available in the forms of transformations or can be constructed from transformations. For these, see the manual for the "@" transformations.