Does anybody know how I would make an object disappear when it is clicked using coordinates? I have another object blocking it so it can't directly be clicked.
When the mouse was pressed, you can get the current location of the mouse with the use of the MouseInfo object.
Then you can either check if the mouse X and Y coordinates are between xMin/xMax and yMin/yMax (if cellsize>1 at least) and remove your object then.
Or you move an invisible helper object to the position of the mouse, get a list of all object in a small range with the getObjectsInRange method and if your object is one of them, remove it.
(To see the methods and how they are used, visit the API with this link https://www.greenfoot.org/files/javadoc/ or by double clicking on Actor/World in Greenfoot.)