Yes! You can do this with the Power Spectral Density (PSD) option on transmitter objects (under Transmitter Properties > Basic > Definition > Modulator tab) and radar objects (under the Radar Properties > Basic > Definition > Mode tab > Waveform tab > Modulator tab).
The STK Communications Module will produce waveforms for built-in modulations, or you can import data using an external modulator file or use a plugin to define arbitrary waveforms. The PSD option will kick RF filter analysis into a high-fidelity mode, where waveforms are filtered to produce modified (updated) waveforms at the transmitter output or the receiver input. Here is the STK documentation on
modulators.
Radar currently uses only one built-in PULSED waveform. However, jamming transmitters can have arbitrary waveforms, and STK will compute the interactions at the radar receiver.
Another thing to note is that the sampling rate is adaptive based on the bandwidth. The user-defined waveform (frequency domain) samples do not have to be uniformly spaced (fixed step). STK will sample and interpolate the data as needed.
You can learn more about how STK uses RF spectrum filters at:
STK Help > Add-on Modules > Communications & Radar > Technical Notes > RF Spectrum Filters