I have a mat which has different thickness at different locations. How can I model that ? 

This can be done by creating control regions. You can define as many control regions within your mat boundary as you wish. Boundary represents your entire mat and it can have holes or control regions within it. Control region is a region within the mat ( or boundary ) that may have different properties than the rest of the mat. For example a control region can have a different thickness or a different soil property associated with it. Holes are used for defining openings within the mat ( or boundary ). 

One you define a boundary for your mat, please follow the steps listed next to define the control region

1. Add a meshing region from within Mat foundation Job > Mesh Generation > Add Meshing Regions to define the region of different thickness.
2. Go to the Meshing Setup.
3. Click on the boundary name within the tree structure ( mesh1 in the figure below )
4. Now within the graphics screen, select the meshing region defined in step 1. It will turn red when selected.
5. Add selected region as Control Region by choosing the appropriate radio button, putting a name for the region identifier and clicking on Add ( see figure below )
6. The name of the control region would now show up under the boundary name in the tree as shown.
7. Add as many control regions as needed following steps 1 to 6.
8. Once the control regions are generated, you would need to regenerate the mesh.

Once the control regions are defined, go to Analysis Properties > Slab thickness and assign the required thickness to the boundary or the control regions.