The problem of covariance estimation for replicated surface-valued processes is examined from the functional data analysis perspective. Considerations of statistical and computational efficiency often compel the use of separability of the covariance, even though the assumption may fail in practice. We consider a setting where the covariance structure may fail to be separable locally-either due to noise contamination or due to the presence of a nonseparable short-range dependent signal component. That is, the covariance is an additive perturbation of a separable component by a nonseparable but banded component. We introduce nonparametric estimators hinging on the novel concept of shifted partial tracing, enabling computationally efficient estimation of the model under dense observation. Due to the denoising properties of shifted partial tracing, our methods are shown to yield consistent estimators even under noisy discrete observation, without the need for smoothing. Further to deriving the convergence rates and limit theorems, we also show that the implementation of our estimators, including prediction, comes at no computational overhead relative to a separable model. Finally, we demonstrate empirical performance and computational feasibility of our methods in an extensive simulation study and on a real dataset. Supplementary materials for this article are available online.