By applying plasma for short time, cleaning of Si substrate may be done. 

Dear Duni C Thakur,

Si wafers/substrates can be clean in-situ with a thermal cleaning proceeding. For that you can ramp-up the substrate temperature up to 900 ºC, and maintain it for 5 min. This will be enough to decompose the native oxide layer and let a clean Si surface.

For a lower cleaning temperature, you can make a wet cleaning followed by a in-situ thermal cleaning. For the wet baths you can use the following proceedings: piranha, RCA I, RCA II. In the end you are going to have a clean surface with a very thin SiO2 layer. Immediately after the wet cleaning the substrate should be introduced in the chamber. Now, the thermal cleaning can be done at 700 ºC for 5 min.

The thermal cleaning at 900 ºC consumes less time but because of the high temperature can lead to thermal faceting of the silicon surface.

The wet cleaning + thermal cleaning e more efficient removing carbon base, and metal contaminants but consumes substantially more time (wet cleaning is at least  1h30). This method can be more interesting for electronic device applications.

Both these methods are used in molecular beam epitaxy to clean and prepare Si wafer for layers growth.