Methods and apparatuses for programming non-volatile semiconductor memory devices by using modulated pulses are disclosed. An apparatus may have a pulse generator, to create a sequence of pulses and set a threshold voltage of a non-volatile memory cell, and a pulse coupler. The apparatus may have 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 apparatuses may modulate the pulse durations early in the sequence when programming fast bits and late in the sequence when programming slow bits. An apparatus may generate a sequence of pulses, apply the sequence of pulses to a memory cell to set a threshold voltage of the memory cell, and modulate one or more of pulses in the sequence the parameters of pulse duration, pulse separation time, and step voltage magnitude.