Two-point correction-based nonuniformity correction of a scan-based long wave infrared camera can be successful in normal working environments. However, the method produces strong fixed-pattern noise in cluttered aerial environments. We analyze the mechanism of such phenomena and propose a nonuniformity correction method by combining a reference-based approach and a nonlinear filter-based residual offset estimation method. The nonlinear filtering process of row directional minimum filtering after two-point correction can remove the nonuniformity around cluttered aerial infrared images. Experimental results validate the feasibility of the proposed method.