By strong acid treatment you can functionalize the Surface SiO2 to Si-OH and then use  (3-Aminopropyl)triethoxysilane, (3-Mercaptopropyl)trimethoxysilane. Whatever the XXX- functionalization you want, you can do with 3-XXX-propyl)trimethoxysilane. 

You can follow these steps :

Substrate Surface Cleaning(Crucial Step):

This is the preparative step, chronologically   include placing the substrate  in the chromic acid solution overnight, keeping  of  the substrate (after drawnout from cromic acid)  in warm water for 10 min which will be repeated three times, sonication of substrate in Millipore water which will also be repeated three times and then  finally overnight placing of the substrate in the vacuum oven at 60˚C .

Substrate Slilnization:

The Visually Cleaned substrate is then dipped into the 10% solution of APTES in ethanol for 30 minutes and then three times sonication and rinsing in ethanol solution for 10 mins  and finally sonication and rinsing in Millipore water. Then the rinsed out substrate is kept in vacuum oven at 60˚C for overnight for condensation.

Then you are done. 

The procedure of Abhishek is a good example of "know-how" and will work quite well especially for the basic APTES. If you keep the mechanism in mind (siloxane publication) multiple other ways will also lead to the goal (You need water and catalyst and a thin primer layer). I suggest using a less toxic, residue-free cleaning procedure (like H2O2/H2SO4) and a gase phase siloxanisation (acid surface and humidity works quite well) This a very simple, fast procedure using a desiccator, silane, reduced pressure and an (acid activated or a new) cleaned wafer surface, SiO2 (and atmospheric humidity). I also published some influences of "dry"(new) and "wet"(acid surface) preparation using APTMS and APTES resulting in m-APS.

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