Although, I have not  used Ni/SiO2 substrate for growing graphene but still I think you should have to increase the F3Cl3 concentration. A higher concentration of FeCl3 will remove the Ni quickly and your sample PMMA/graphene can float on the surface of the FeCl3 liquid. But you should have to take care about the quality of graphene film since a fast etching rate of Ni can tear the graphene also. I hope this will help you.

Dear Sibel Kasap, Yes, You can also use Bubbling Transfer Method for Large Scale High Quality Graphene Etching and Transfer. Please study following articles for this:

http://pubs.acs.org/doi/abs/10.1021/nn203700w

http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1702.html

One more thing. If you're going to use the old method (i.e. via FeCl3), then you should use more concentrated FeCl3, instead of increasing its magnitude (for some reasonable scale of up to 5 cm x 5 cm). Although, 1 M concentrated solution is enough for small samples like 1 cm x 1 cm or 2 cm x 2 cm but you can use more concentrated if films are not being separated. If solution is such enough that the Nickel with Graphene/PMMA is completely dipped in the solution, then no need to further increase the quantity of solution.

If you use a higher concentration of FeCl3, etching would be faster. Otherwise, you have to wait at least 20 hrs to have it completely etched. I usually use 15-20 gr of FeCl3+60 ml of water, and after 6 hours, Ni is fully etched and graphene is perfectly transferred.