For incoherent scatter measurements, the effective subtraction technique is to alternate the duration of amplitude-modulated signals between a pair of consequently radiated pulses. The resulting gain of spatial resolution enables us to steadily assess the electron density profile by the Faraday rotation method. The paper describes the electron density measurement technique, which involves analyzing narrow-band signals from Irkutsk Incoherent Scatter Radar, and proposes an automated method of determining the electron density for the problem in which the convolution of the radiated signal waveform with backscatter signal cannot be neglected. The inverse problem of electron density recovery is considered as a standard nonlinear optimization problem, which is solved using the algorithms for global and local optimization applied consequently. We compare the electron density profiles obtained by analyzing different pulse waveforms and from Irkutsk ionosonde data.