Multimode photon subtraction provides an experimentally feasible option to construct large non-Gaussian quantum states in continuous variable quantum optics. The non-Gaussian features of the state can lead towards the more exotic aspects of quantum theory, such as negativity of the Wigner function. However, the payoff for states with such delicate quantum properties is their sensitivity to decoherence. In this paper, we present a general model that treats the most important source of decoherence in a purely optical setting: losses. We use the framework of open quantum systems and master equations to describe losses in n-photon-subtracted multimode states, where each photon can be subtracted in an arbitrary mode. As a main result, we find that mode-dependent losses and photon subtraction generally do not commute. In particular, the losses do not only reduce the purity of the state, they also change the modal structure of its non-Gaussian features. We then conduct a detailed study of single-photon subtraction from a multimode Gaussian state, which is a setting that lies within the reach of present-day experiments.