SEM is a surface scanning technique. it works only by the emission of secondary electrons from few micrometer depth of the sample. therefore 1mm thick samples are more enough. however you can manipulate the energy of electron beam for thinner samples. mostly it is being done on steel or aluminium stabs being used. in case of polymeric films you can peel them and scan.
For surface microstructure, the average surface roughness of the substrate is important. For sub-micron thick films, polished Si wafer, glass substrate or fine-polished metal maybe used. A substrate size of 1 um2 and thickness of about 1 mm is sufficient.
For cross-section view, the sample (after film deposition on Si or glass) can be fractured to expose the cross-sectional area. Alternatively, the sample can be cold mounted (in standing position) and then sectioned to expose the cross-section followed by grinding/polishing for better view.
Selection of Substrate is depend upon application purpose, either you are planning to do some optical analysis or some electrical analysis. To get high micro-graphs resolving on glass down to some 10-20 nm features you need a conductive sputtering(gold sputter coating) on the glass substrate. but if you deposit you film over metallic glass(Fe54B13Si3) there is no need to sputter gold or silver coating on your substrate.
Silicon has no such kind of grounding problem You can use standard Si wafer to deposit TiO2 it give better resolution at nano level. The size of Si substrate could be 5x5 mm (length- Width) and 250-500 μm thickness.For glass substrate you can use 5 mm × 5 mm × 1.1 mm (L × W × Thickness). Detailed information about Matellic glass in given here; http://psroc.org/cjp/download.php?type=paper&vol=18&num=1&page=43
you can get example here:
TiO2 over SiO2/Si- http://www.mdpi.com/sensors/sensors-13-09513/article_deploy/html/images/sensors-13-09513f4-1024.png
TiO2 over Slide Glass- https://openi.nlm.nih.gov/imgs/512/334/3296554/PMC3296554_1556-276X-7-89-2.png
You can analyze any material that exhibit good electrical conductivity (metals) and semiconductors with high conductivity, which do not charge electrically when impacted by the electrons from the SEM electron imaging beam. If you want to analyze insulating materials, you need to put a very thin coating of gold or any other metal (40-50 nm thick may be enough ) on the top surface of the sample and going around to the bottom of the sample to make contact with the electrically conductive substrate holder, in order to avoid charging by accumulated electrons in the material, which strongly affect the resolution of the image, which gets blurry when charging. The largest size of a sample you can introduce into your SEM depends on the substrate holder. SEM for research in Universities, general do not have holders that can hold large area wafer like those used in the semiconductor industry (200 to 300 mm in diameter wafers). Some universities may have SEM systems that can hold up to 100 mm diameter wafers. Many semiconductor fabs have SEMs that can hold large area wafers, since they use the SEM to characterize the surface morphology of integrated circuits once built.