Two filters for improving the visibility of crystalline material in the presence of amorphous surface contamination layers in high-resolution electron microscope images can be constructed automatically from the information present in the Fourier transform of the recorded image. The recorded signal is considered in the first approximation to be the sum of two signals which are uncorrelated in the frequency domain. By estimating the power spectrum of the signal from the amorphous layer, an optimized estimate for the desired signal is given by the Wiener filter. A second filter which uses the estimated amplitude of the amorphous signal to subtract out a background can be shown to be related to the Wiener filter. The two filters are applied to an experimental image of zeolite and the effects of the two filters are compared.