The nanoscopic characterization of ferroelectric thin films is crucial from their device application point of view. Standard characterization techniques are based on detecting the nanoscopic charge compensation current (switching current) caused by the polarization reversal in the ferroelectric. Owing to various surface and bulk limited mechanisms, leakage currents commonly appear during such measurements, which are frequently subtracted using the device I–V characteristic by employing a positive-up-negative-down measurement scheme. By performing nanoscopic switching current measurements on a commonly used ferroelectric, BiFeO3, we show that such characterization methods may be prone to large errors in polarization estimation on ferro-resistive samples due to current background subtraction issues. Specifically, when the resistance of the ferroelectric thin film is associated with polarization reversal, background current subtraction is not accurate due to the mismatch of the I–V characteristics for two polarization states. We show instead that removing the background current by an asymmetric least-squares subtraction method, though not perfect, gives a much better estimation of the ferroelectric properties of the sample under study.