We investigate the use of multilevel Monte Carlo (MLMC) methods for estimating the expectation of discretized random fields. Specifically, we consider a setting in which the input and output vectors of the numerical simulators have inconsistent dimensions across the multilevel hierarchy. This requires the introduction of grid transfer operators borrowed from multigrid methods. Starting from a simple 1D illustration, we demonstrate numerically that the resulting MLMC estimator deteriorates the estimation of high-frequency components of the discretized expectation field compared to a Monte Carlo (MC) estimator. By adapting mathematical tools initially developed for multigrid methods, we perform a theoretical spectral analysis of the MLMC estimator of the expectation of discretized random fields, in the specific case of linear, symmetric and circulant simulators. This analysis provides a spectral decomposition of the variance into contributions associated with each scale component of the discretized field. We then propose improved MLMC estimators using a filtering mechanism similar to the smoothing process of multigrid methods. The filtering operators improve the estimation of both the small- and large-scale components of the variance, resulting in a reduction of the total variance of the estimator. These improvements are quantified for the specific class of simulators considered in our spectral analysis. The resulting filtered MLMC (F-MLMC) estimator is applied to the problem of estimating the discretized variance field of a diffusion-based covariance operator, which amounts to estimating the expectation of a discretized random field. The numerical experiments support the conclusions of the theoretical analysis even with non-linear simulators, and demonstrate the improvements brought by the proposed F-MLMC estimator compared to both a crude MC and an unfiltered MLMC estimator.