A regeneration system includes a first comparison module that at least one of (i) compares a first temperature of an adsorber to an adsorber release temperature and (ii) compares a second temperature of an engine to a predetermined temperature, and generates a first comparison signal. A second comparison module that compares a particulate matter output of the engine with a predetermined output and generates a second comparison signal. A mode selection module that selects a mode and generates a mode signal based on the first comparison signal and the second comparison signal. A bypass valve control module that adjusts position of a bypass valve to bypass at least one of a particulate matter (PM) filter and the adsorber based on the mode signal.