How to remove other apps icons (like Skype or WhatsApp) from contact and phone app?

I would like to keep Skype Mobile installed but get rid of its icons from contacts **AND/OR** from being asked whether I want to make a call to the contact through Skype or other similarly annoying application. Is there any facility in Android that allows me to keep the control of that? Uncle Google isn't much helpful in that matter. Moreover I have two Skype icons per contact on my phone. And that the thing that hits my taste. Phone details: Sony Xperia S, Android 4.1.2