custom click to call implementation in mscrm 2013, currently dynamics crm 2013 built in support for Skype and lync. Is there any way I can override this behaviour so that call will be made from my telephony application. Is there customization support for this ?
You can't override the default behavior for phone fields that has Skype/Lync integration.
The alternative is to build a WebResource that will display the phone number and implement your click to call, or create a command button (ribbon) to handle the call.