FFT with fewer outputs than inputs
The FFT is just an implementation of the DFT, which is an invertible operation on any vector composed of complex numbers.
Since invertible operations need to be surjective:
No, an FFT can't have less outputs than inputs.
You are, probably, looking for something that &quot;condenses&quot; your data, e.g. looking for features, or projecting onto a smaller vector space that is sufficient to describe your signals of interest; keywords you might be looking for would be &quot;feature extraction&quot; or &quot;compressive sensing&quot;.
However, I think it might be sensible for you to post a new question, describing exactly what you actually want to do (and not focused on employing the FFT itself).