In this work, we describe the calibration and first measurements in the commissioning of MuTe, a hybrid Muon Telescope with two subdetectors --a scintillator hodoscope and a Water Cherenkov Detector (WCD)-- for imaging the inner structures of Colombian volcanoes. The hodoscope estimates the trajectories of particles impinging on the front and rear panel, while the WCD acts as a calorimeter for the through going charged particle. MuTe combines particle identification techniques so as to discriminate noise background from data. It filters the primary noise sources for muography, i.e., the EM-component ($e^{\pm}$) of Extensive Air Showers (EAS) and scattered/upward-coming muons. The WCD identifies Electrons/positrons events by their deposited energy identifies, while scattered and backward muons are rejected using a pico-second Time-of-Flight(ToF) system. Muon generated events were found in the deposited energy deposited range of ($144$MeV$ < E_d <$ 400MeV), represent only about the 40$\%$ of the WCD-hodoscope acquired events. The other 60$\%$ of data is composed by ($e^{\pm}$) events under 144 MeV and multiparticle events above 400 MeV. Subsequently, low-momentum muons ($<$ 1 GeV/c), which are scattered by the volcano surface, measures a ToF $>$ 3.3 ns for traversing one meter length.