Perhaps you may try to use blocking electrodes and calculate back the properties of your layer form the measured sanwich. I do not know how well it works with nanolayers.

Could it be that sputtering connected the bottom and the top electrode (unintentionally)?  Sputtered atoms can have a wide angular distribuion and can "bounce" into the side or even the bottom of a substrate. 

Because your film is relatively thin and vulnerable, the deposition of the second electrode by any means will likely damage your film. In this case, it will be better not to deposit a second electrode. I would use the interdigitated electrodes deposited on the the glass or well polished high resistance silicon wafer. After you deposit your film over the electrode system you could measure the admit ace at different frequencies. From these measurements you can calculate the dielectric constant and other properties of your film. You can also use a film with very known dielectric properties to calibrate your system. 

Thank you all for the suggestions.

Dear Vitaly Sir,

           I did understand what you wanted to say, however, I am not totally clear about how should we make interdigitated electrodes experimentally in our lab. 

Hello, Anup,

There are a few companies distributing the  intergigitated electrodes. For example,

Dropsens,

http://www.dropsens.com/en/interdigitated_electrodes.html

Laboratory Products

http://www.abtechsci.com/labproducts.html

You could also make them yourself if your Institute has the capability of vacuum deposition and lithography for making masks for the interdigitated electrodes.

There is a link to the article describing the fabrication of these electrodes:

http://inee.unimap.edu.my/wp-content/uploads/2015/01/ide.pdf

Good luck,

Vitaly

You could try a Hg probe:http://www.mdc4cv.com/mercuryprobe.htm

and a CV analyzer.  If the film is highly conductive, the analyse will tell you so.  300nm is thick for Si02 film.  The FTO should be fine as a substrate for the Hg probe.