Photon-counting detectors are greatly improving the resolution and image quality in computed tomography (CT) technology. The drawback is, however, that the reconstruction becomes more challenging. This is because there is a considerable increment of the processing data due to the multiple energy bins and materials in the reconstruction analysis, as well as improved resolution. Yet efficient material decomposition and reconstruction methods tend to generate noisy images that do not completely satisfy the expected image quality. Therefore, there is a need for efficient denoising of the resulting material images. We present a new and fast denoiser that is based on a linear minimum mean square error (LMMSE) estimator. The LMMSE is very fast to compute, but not commonly used for CT image denoising, probably due to its inability to adapt the amount of denoising to different parts of the image and the difficulty to derive accurate statistical properties from the CT data. To overcome these problems we propose a model-based deep learning strategy, that is, a deep neural network that preserves an LMMSE structure (model-based), providing more robustness unseen data, as well as good interpretability to the result. In this way, the solution adapts to the anatomy in every point of the image and noise properties at that particular location. In order to asses the performance of the new method, we compare it to both to a conventional LMMSE estimator and to a "black-box"CNN in a simulation study with anthropomorphic phantoms.