What DSP techniques can be used to change the timbre of complex tone? I'm experimenting with applying unusual 'spectral mangling' type special effects to audio.   

1)  What DSP techniques can be used to change the timbre of a complex tone, such as that produced by the voice, or a musical instrument?    


Are there any ways to manipulate the level of specific frequencies in the spectral profile of a complex tone. E.g. Assuming a tone with a fundamental frequency of 440 hz, use some DSP method to augment, for example the 2nd harmonic overtone at 1320Hz Khz, or remove another peak at say, 3Khz).   
What's the best way to remove specific frequencies, or as narrow bands of frequencies as possible using DSP?


I use mixing/mastering, offline, and real time DSP VSTs, standalone programs, outboard effects units, but am interested in any methods which could work.

2) What alternatives (if any), are there to using techniques which introduce significant ringing or other artifacts which degrade the sound?

3) Are there any ways to 'clean up' audio after processing, removing artefacts which have been introduced?
Phase vocoders with custom resynthesizers can be used for this, as in time pitch stretching code that attempts to preserve the spectral formant envelope.  But phase vocoder analysis/resynthesis is not artifact-free.