Abstract-We investigate the impact of spectral filtering in mode-locked fiber lasers with an extended geometrical model. Our iterative model, which includes gain, loss and the pulse shaping effects of chromatic dispersion and selfphase modulation, is used to model the laser cavity dynamics. Simulations show that broadband pulses experience large losses from spectral filtering in the cavity, leading to a number of potential laser instabilities and outcomes such as multi-pulsing, periodic and chaotic states, or a single pulse which transitions to a higher energy state. For narrow band spectral filtering, the laser dynamics is dominated by the gain-loss dynamics in the cavity which causes multi-pulsing. For broadband spectral filtering, the nonlinearity induced spectral reshaping of the single pulse can lead to a discontinuous pulse energy transition that circumvents multi-pulsing. The inclusion of third order dispersion shows that the multi-pulsing instability is induced even in the case of broadband spectral filtering.