Massive multiple-input-multiple-output (MIMO) systems can suffer from coherent intercell interference due to the phenomenon of pilot contamination. This paper investigates a two-layer decoding method that mitigates both coherent and non-coherent interference in multi-cell Massive MIMO. To this end, each base station (BS) first estimates the channels to intra-cell users using either minimum mean-squared error (MMSE) or element-wise MMSE estimation based on uplink pilots. The estimates are used for local decoding on each BS followed by a second decoding layer where the BSs cooperate to mitigate inter-cell interference. An uplink achievable spectral efficiency (SE) expression is computed for arbitrary two-layer decoding schemes. A closed form expression is then obtained for correlated Rayleigh fading, maximum-ratio combining, and the proposed large-scale fading decoding (LSFD) in the second layer. We also formulate a sum SE maximization problem with both the data power and LSFD vectors as optimization variables. Since this is an NP-hard problem, we develop a low-complexity algorithm based on the weighted MMSE approach to obtain a local optimum. The numerical results show that both data power control and LSFD improve the sum SE performance over single-layer decoding multi-cell Massive MIMO systems.