In fourier space, how to apply transfer function with n frequencies to input data with m>>n frequencies I have a transfer function in Fourier space with $N=2028$ frequencies $(\frac {0, 1}{(N\cdot dx)} \dots ) $

Where $dx = 0.1m$. 

I need to apply this transfer function to a signal with 20000 samples (also $dx=0.1m$). 
When I transform this signal to Fourier space I get 20000 frequencies.
 So, the sizes don't match. What do I need to do to be able to apply the transfer function (i.e. to multiply the Fourier transforms)? I guess, I could just remove the first $20000-2028=17952$ frequencies from the Fourier transform of the input signal, since they are not present in the transfer function.

But is that correct?
For the signal that is shorter than the other, before you FFT it, zero-pad it so that the length is the same as the other.