In the present work, we propose a generalization of the confidence polytopes approach for quantum state tomography (QST) to the case of quantum process tomography (QPT). Our approach allows obtaining a confidence region in the polytope form for a Choi matrix of an unknown quantum channel based on the measurement results of the corresponding QPT experiment. The method uses the improved version of the expression for confidence levels for the case of several positive operator-valued measures (POVMs). We then show how confidence polytopes can be employed for calculating confidence intervals for affine functions of quantum states (Choi matrices), such as fidelities and observables mean values, which are used both in QST and QPT settings. As we discuss this problem can be efficiently solved using linear programming tools. We also demonstrate the performance and scalability of the developed approach on the basis of simulation and experimental data collected using IBM cloud quantum processor.