I often switch my print material, i.e. ABS / PLA / Wood / Flex,
How can I best clean out my extruder between them to ensure I don't contaminate my next print?
In most cases, removing the old filament from the printer, inserting the new filament in, and running the new filament through the printer for a short period of time will clean the nozzle. The skirt of the print can also be a time during the actual print for the old filament to be flushed. Assuming the skirt is long enough, all that needs to be done is the new filament inserted and the print started.
Assuming that extruding new filament does not fix the problem, there is a more serious problem such as a clogged extrusion head that needs to be fixed with other methods.