hi there...is your solution spread well on FTO? i mean just try to place a drop of your coating solution, and you will know whether it spread or make a hemisphere...if hemisphere, than the coating material doesnt wet to FTO well...so with the spin coating what you observe could be on edges...to avoid non-wetting, either need to modify the FTO surface, or use some additive in the solution to reduce the contact angle...last but not the least, visually you maynt observe a film on FTO, if that happen to be really thin...do the transmittance/reflectance with the reference sample...

My aim is to drop my PVK on to the FTO coated glass substrate and then thermally evaporate an electrode on to it. Mostly what is happening is that my electrode is shorting with the FTO layers since, in my opinion, a part of the FTO is touching the electrodes, but what is surprising is that when I do an AFM imaging on my simply spin coated sample, I get peaks of 100nm at every micron almost periodically [img attached]...when I do the surface profile of only FTO, also I get peaks and crests sometimes greater than 100nm, I am unsure whether trying to spin coat a film less than 500nm thick on FTO is a good idea, or should I go for ITO instead.

hi there...FTO or ITO doesnt make any difference on surface...both are conducting substrates...but sometime you have to check for the stability of the film under thermal or plasma environment...i mean one of them degrades faster than the other...the periodic hump of ~80nm could be due to polymer solution...quantum dots, if aggregate during the process quite unlikely make that hump, if dots are less than 10nm...btw for making electrode and than using that for any contact, you need to be extra careful, how can you make sure there was/were not any pin holes on the surface, so once evaporation finished the electrode get shorted...use some mask , do some metallisation for I-V or any such study...