Well, let me know what kind of the organic molecules, is it macromolecule, polymer molecule, polar or non-polar molecules, etc. It is because surface morphology of any material is tightly influenced by typical interactions occur between the molecules and its substrate. In your case, SiO2 substrate is polar in properties so you should use hydrophilic organic molecule-based materials with various concentration and volume to obtain a good 2D surface morphology. rather than varying temperature.

Dear Pratama Juju

Thanks for the response. The organic molecules i am using is derivatives of Diarylethene photochromic Molecules. You mean i have to do surfacetreatment like PMMA or HMDS first and then deposit the organic material. 

Thats a pretty wide range of compounds you describe there. Do you have to vapor deposit them? 

But I guess what wibawa means is that the surface energies of your sio2 and your compounds have to match in order for the molecules to "wet" the sio2. So if your molecules are hydrofobic you need a hydrofobic coating on you sio2. 

Cheers 

Dear  Soren Thanks for your use full answer.

i using thermal deposition at high vacuum to deposit the molecules. 

Which are beast hydrophobic Coating available. can i use PMMA or HMDS

Again, you might not need the most hydrofobic  coating to get the best result. The coating which is most similar to your molecules should be the best. 

Cheers