I don't think CHS can stop other applications seeing new clips, but it has a feature to ignore clips coming from certain applications, if that's what you mean. Bring up the main window and go View -> Options and select the tab Capture Options. You then find a box labelled "Ignore these applications (just filename, each on separate line, e.g. notepad.exe)" and enter the names of the programs you want ignored. Mine contains, inter alia, keepass.exe, pins.exe, etc.
HTH.