I have prepared a thin film of PEDOT:PSS over SiO2 substrate. I tried masking the substrate with teflon tape but the solution get stuck near the teflon tape and the thickness there is greater compared to other areas.
Using an optical thin films method of characterization, such as ellipsometry, you should be able to determine the thickness of your film on SiO2.
You can try making a scratch in your film, e.g. with a sharp tip (metal pin, needle), and then use an AFM or profilometer to scan across the scratch.
Ellipsometric measurement would be helpful. Or you can try to make a topography profile by AFM after e.g. reactive ion etching or mechanical removal of the top layer (scraping or scratching).
Other possibility would be to use interferometry microscope setup on the areas where step of your film occurs: formed by mechanical scratch or deposition mask
As Cosmin Farcau wrote, you can scratch the film. Do it with AFM (nanolithography) and then measure the film thickness.
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