> I can not handle the yellow/green ish colors.
MatterControl does not yet have the ability to pause the print at a certain point, but that feature is on our short list for development so you can look for that in the next few months.
In the meantime, I think you're on the right track with the M0 command, although this only pauses for a specified amount of time so I don't think this is what you want to use. Also, your printer must be running firmware that supports the command-- which if you haven't flashed it with anything else should be running Marlin firmware by default which does support the M0 command. See the RepRap GCode article for specifics on which commands are supported by which firmwares and for general reference of commands.
That said, perhaps you did not issue the correct parameters after the M0 command? Not only must you issue 'M0', but also then specify how long you want the print to pause for afterward. Like so:
Where Pnnn = P[milliseconds].
In any case, MatterControl has some commands which can be used in GCode or in the Custom GCode fields I'll explain in a moment:
These are unique to MatterControl and can be inserted directly into GCode which MatterControl reads. I suggest you use @PAUSE instead of M0, which as I explained before, has a hard time limit.
The other way to accomplish this pause is to do it manually-- which I recommend in this circumstance since you'll physically be there to change the filament or whatever you're doing. MatterControl has a 'Pause' button which shows while the print is running. Clicking it will, by default, pause the print at exactly where the nozzle is at that time. But, then you can get creative.
You'll use one of MatterControl's custom GCode settings -- Pause GCode -- to give the printer some custom instructions for when you hit the Pause button. Navigate to 'Settings & Controls -> Settings -> Printer -> Pause G-Code' and enter something like:
Then, when you hit Pause, the nozzle will move up 40 mm and over 60. Change the filament or whatever you need to do, then when you hit the 'Resume' button the nozzle will return to the coordinates it was at when the print was paused and continue printing.
For reference, any valid GCode commands can be entered in the Custom G-Code section, but be careful what commands you enter. The printer will follow instructions explicitly, and bad instructions can damage your printer. If in doubt, test your GCode using the GCode Terminal (Settings & Controls -> Options -> Hardware Settings) before you enter it in a Custom G-Code field.
EDIT: Added @ command information, formatting.
EDIT 2: Changed @PAUSE, etc. to lower case