Methods and apparatuses for programming non-volatile semiconductor memory devices by using modulated pulses are disclosed. Embodiments generally comprise a pulse generator, to create a sequence of pulses and set a threshold voltage of a non-volatile memory cell, and a pulse coupler. Alternative embodiments may include a threshold verifier capable of verifying that the threshold voltage is set within an acceptable voltage range of a target threshold voltage. A pulse width modulator in some apparatus embodiments may modulate the pulse durations early in the sequence when programming fast bits and late in the sequence when programming slow bits. Method embodiments generally comprise generating a sequence of pulses, applying the sequence of pulses to a memory cell to set a threshold voltage of the memory cell, and modulating among pulses in the sequence the parameters of pulse duration, pulse separation time, and step voltage magnitude.