Yes in BlueKenue you can select a node and right click to Edit Selected Node. This is fine for editing limited number of nodes individually. If you would like to edit a group of nodes in an area, you can create a polygon enclosing the area and set the polygon to desired value. Then you can map the polygon to the bathymetry mesh. The mapping operation will edit bathymetry values inside the polygon. Hope this helps,
Hailiang