I need help to build a patch that would change the timbre of a played/recorded instrument, in such a way to match the timbre of another one.
This is to make one instrument sound like another one (both instrument timbres are known).

Can you please help me get started and point me to the right direction.
How would one start to create such a patch in Pure Data?

Ah easy as that... Generally you just have to:
Place the right objects and connecting them correctly...;)

Haha...

that sounds like an fft job. Have a look at the helpfiles in the helpbrowser : Pure Data/3.audio.examples/I06.timbre.stamp.pd