The use of counter-propagating sub-picosecond pulses to modify the temporal shape and spectrum of a probe pulse in an SOA is investigated using a modified nonlinear Schrödinger equation (MNLSE), which includes all of the dynamical processes relevant to the sub-picosecond range. The MNLSE is solved using a novel numerical method based on trapezoidal integration and central difference techniques. It is shown that by using the counter propagation scheme besides amplification, both time and spectral profile of the propagated pulse are compressed. Furthermore, the output pulse distortion caused by nonlinear phenomena in SOA is improved. ©2009 IEEE.