When you work with maps, geojson format is one of the most important format to use.
But the transformation / edition of it is not easy. A solution is to use a JS library like turfjs to have a programatic solution. But, sometimes, the programatic solution is not a quick win. For instance, to subtract two geojson, specific CLI tools can be the solution: geojson-cli-difference
npm install -g geojson-cli-difference
cat world.geojson | geojson-cli-difference water.geojson > land.geojson