The list of experiments is certainly not linked to the thorlabs equipment - I hope you'll find it useful! Keep us updated about what you finally realized in your lab!
An interesting experiment (my students were happy) - tapping mode visualization of a blood smear. The preparation is very simple - put a droplet of blood (from the bravest student :)) to a glass slide and make a smear:
https://www.youtube.com/watch?v=JgUwcGQF8CE
RBC are pretty stable without any chemical fixation and it is possible to take some nice pictures.
You can measure pore size or pore size distribution of different porous materials. I have completed such work in my masters work and published in a reputed journal. I have used phase imaging, height diagram in tapping mode to detect pores. I think my work is very much similar to what you are thinking.
Here is the link:
Article An Approach for Quantitative Analysis of Pore Size Distribut...
If you wanted to include something more advanced than simple topology, you can easily use calibration samples for either surface potential or magnetic force experiments, where experimentally the work is straightforward (calibration samples for surface potential are e.g. close regions of Al/ Si/ Au) with good contrast, but there is more interesting theory behind it. MFM works very well on pieces of old computer memory as well.