Can anyone tell me how this surface looks like 3d which covers red sphere and blue cylinders. 
see the blend file here https://blend-exchange.giantcowfilms.com/b/3570/
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$\begingroup$ There are many ways to approach the rendering of a surface. What aspects are you most interested in? The more you see the surface, the less you'll see the mulecular structure. Is it a choice to show only the surface in 3D and leave the structure as it is? Can you tell more about your goals? Do you have any reference image? $\endgroup$ – Carlo Jul 22 '17 at 11:35
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$\begingroup$ Hi @Carlo I want somewhat similar to Penicillin structure github.com/patrickfuller/blender-chemicals but not too much glassy. Internal molecular and surface both should be visible clearly. $\endgroup$ – user3704712 Jul 22 '17 at 12:26
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$\begingroup$ perhaps, you could try to build it with metaballs, then you could convert them to mesh... $\endgroup$ – m.ardito Jul 22 '17 at 12:33
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The primary problem with the lack of visual space is that you're using an Emission Shader for the blue and the red. Emission shaders cannot receive shadows so they look more cartoony for something like this. I would change the material to Diffuse:
I added a UV Sphere with a Solidify Modifier and mixed the Glass Shader with Transparent (mostly transparent) to take the "edge off the glassiness".
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$\begingroup$ Thank you very much @bertmoog for your good answer. I am trying to repeat what you have done but not getting the same. Can you upload the blend file so that I can see what is the difference between my blend file and your blend file. Thanks a lot. $\endgroup$ – user3704712 Jul 22 '17 at 18:17
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$\begingroup$ @user3704712 - No problem: blend-exchange.giantcowfilms.com/b/3573 - Just open it and press Shift+Z to see render preview. $\endgroup$ – bertmoog Jul 22 '17 at 18:31
