Why do I can't do union or do another geoprocessing two shapefiles with different CRS in QGIS? For example, I want to do union two shapefiles, one shp with CRS WGS84 and another shp with CRS WGS84/UTM 47N. It can't be happened and a message box will appears. Even though this process can be done in ArcGIS. I'm using QGIS 2.14 Essen. Any suggest?
QGIS works for defined projection in each layer and does not work with layers with different projections. Even if you see the two layer overlay each other due to the on fly projection is enabled, the on fly projection in QGIS does not disable the original projection defined in the layer. Therefore, if you want to do any geoprocessing task, the two layers should have the same projection in order to get a successful result.
You can simply right click one of the two layers and go to save as, and in the 'save as' dialog box choose the target projection which should be similar to the second layer. Then do the geoprocessing task that you want.