Program Extents

I'm new to CNC. I installed LinuxCnc and have it configured correctly hopefully. I'm able to jog,I have my table limits setup. I have my limit switches setup to home. My machine goes to its home position without a problem. I'm trying to run a program created in Fusion 360, its for a vacuum table I would like to build. When I try to run the program I get an error message "Program exceeds machine maximum on-axis Z " In the preview plot it's clear that I've exceeded the soft limits but I can't figure why this is happening. I suspect this has to do with offsets. If I try to run some sample code I've found on Thingiverse the same thing happens. I have 2 screenshots that show whats going on. ANY HELP to point me in the right direction would be greatl appreciated.

Yes in my Stepconf I have Pin 13 set for Home Z invert is checked and my Z-Axis Table travel -3.5 to 0.0 is this where I am making my mistake. And if yes could you point me in the right direction to set this up correctly.

Yes, it does.

you need to touch off the part Z

JUST for your
move down Z some space to get view 1inch
and press touch off
then enter and you can run the simulation

for REAL miliing you need to set the G54 Workpice ofset by putting the Tool manuell to the Corner Top and press touch off

Thank You