It would be nice if the Define Map Area box could be rotated to select a given area and/or have the option to use a polygon to draw around a selected area. I use the sediment volume estimation tool frequently and this would help a lot in selecting just the area of interest and not accidentally picking up an adjacent channel, etc. I often work on sites with long crooked channels and its near impossible to get just the area I want without encroaching on other areas of the lake. thanks

See example pic below.

Yes, a polygon selection would be a good tool.

You can create a new Workspace with the same datas. Here you can use the rectangle region selection tool ever again to delete the not required trackpoints. If you reduce the trackpoints to your wish areas, you can process this datas with the sediment volume estimation tool.