The gas flow in a linear plasma reactor and the plasma chemistry during hydrogenated amorphous carbon and graphite etching are investigated via time and spatially resolved measurements of the ion density and CH emission. A convolution of the ion and hydrocarbon density shows the importance of charge transfer in the plasma chemistry which ultimately yields the CH emission. The spatially resolved measurements clearly visualize the plasma expansion in the reactor and its deflection on a substrate. A stagnation zone is furthermore formed in front of a substrate when placed inside an expanding thermal plasma. An increased ion density further upstream from the substrate is attributed to a reorganization of the gas recirculation cells in the background of the reactor. The movement of a shutter in and out of the plasma expansion likewise affects these recirculation cells. This movement consequently redirects the energy flow to and from the background, as is deduced from the variation in rotational temperature of the CH radical.