I am finding when I import a stl into Slic3r it is using by default the lowest point of the 3d model rather than the models zero point. In my case I generated supports for a DLP print using B9Creator software. The software sometimes creates supports in the negative so my models are usually messed a bit when using that software. Instead of fixing the model it would be great if Slic3r used the models zero point rather than the lowest point as an option. Is there anyway of changing this in the Slic3r? Or possible cutting the bottom couple layers out of the SVG slice file?
Use the "cut" function in Slic3r ("Object">"Cut"). Select the Z height to the desired base and it will delete everything below that height, automatically shifting the model down to put it onto the bed.