This photo shows the ship’s hull mounted so that I can slice a section off the bottom of it to make it a waterline model. The plan is to use a band saw but if this turns out to be too damaging I will have to revert to hand sawing which I feel will be far less accurate in achieving a straight cut on both sides of the hull.
Morpeth In O-Scale 
A trick my carpenter father taught me for when cutting brittle materials; stick a strip of masking tape on, then mark and cut along that – it will help reduce the likelihood of breaking big chunks out of the cut edge, resulting in a much neater finish.
If the cut isn’t perfect, you can try setting it down onto the surface and then using some sort of casting resin to create the water surface this can take up any small variations and fill gaps. Alternatively, attach it to the water base, and use putty to fill up any gaps from the inside before using the resin casting for the water.