We use XMM-Newton blank-sky and closed-cover background data to explore the background subtraction methods for large extended sources filling the EPIC field of view, such as nearby galaxy clusters, for which local background estimation is difficult. We find that to keep the 0.8-7.0 keV band background modeling uncertainty tolerable, one has to use a much more restrictive filter than that commonly applied. In particular, because flares have highly variable spectra, not all of them are identified by filtering the E>10 keV light curve. We tried using the outer part of the EPIC FOV for monitoring the background in a softer band (1-5 keV). We find that one needs to discard the time periods when either the hard-band or the soft-band rate exceeds the nominal value by more than 20% in order to limit the 90% CL background uncertainty to between 5% at E=4-7 keV and 20% at E=0.8-1 keV, for both MOS and PN. This compares to a 10-30% respective PN uncertainty when only the hard-band light curve is used for filtering, and to a 15-45% PN uncertainty when applying the commonly used 2-3 sigma filtering method. We illustrate our method on a nearby cluster A1795. The above background uncertainties convert into the systematic temperature uncertainties between 1% at r=3-4 arcmin and 20--25% (~1 keV for A1795) at r=10-15 arcmin. For comparison, the commonly applied 2-3 sigma clipping of the hard-band light curve misses a significant amount of flares, rendering the temperatures beyond r=10 arcmin unconstrained. Thus, the background uncertainties do not prohibit the EPIC temperature profile analysis of low-brightness regions, like outer regions of galaxy clusters, provided a conservative flare filtering such as the double filtering method with 20% limits is used.