The short answer:
Feed your data in time domain to fftfilt and you will receive filtered data in time domain.
The pedantic answer:
ffftfilt outputs the filtered data in the same domain you put it in. While it is most common to have signals recorded at certain time intervals (thus being in the time domain), you can have all sorts of domains. For instance if you measure a geometric profile, you can have your data at equal distance intervals. Thus your data is in the distance domain. You will have to be aware what the frequencies mean when designing the filter to apply. In the above example, you will need to use space frequencies instead of time frequencies.
Cheers
Manuel
