Stepper motors suffer with skipped steps due to the occurrence of resonance and instability, under certain load conditions. Unlike in other machines, variation of torque is not reflected in the current. Hence the current measurement based position estimation techniques fail. Experimental investigations reveal that high frequency ripples are present in the current dynamics during the resonating periods. This paper proposes an identification technique which works based on ripple content during the transient period of the current rise. It is shown that resonance can be identified and compensated well before the motor misses the step through the excitation voltage. With such compensation, current measurement based estimation techniques provide accurate speed & position estimation. The paper also matches experimental results with the simulation.