Hi Mikael1987
Yes it is possible to replace all pixels with one specific color to another.
Yes it is possible to export each of your tiles to an individual png. eg. you have an animation of 6 tiles/frames and you want to export each frame to a png like so:
You use the tile placer tool (hover for info) and in this case hold CMD+mouse-click on OS X, or Ctrl+mouse-click on windows to add the tiles like i do in this gif, then you choose file->export tileset, tick the box and click export.
As you can see, all my animation has been separated into individual png's.