As per PCI, we need to stop using SSL and TLS(1.0 and 1.1 in certain implementation) from June 30th 2016 as per
We have an client application build on .Net 3.5 which uses HttpWebRequest object to connect to web services.
As per MSDN SecurityProtocolType(https://msdn.microsoft.com/en-us/library/system.net.securityprotocoltype(v=vs.110).aspx) supports only Ssl3 and Tls(1.0) on .Net Framework 4 or below. Tls11 and Tls12 are only supported in .Net Framework 4.5/4.6
Does that mean to be inside Cardholder data environment and fully pci compliant, we need to upgrade all applications to .Net 4.5/4.6 and allow only Tls12 SecurityProtocolType to connect to external web services using HttpWebRequest?
Any communication channel that currently uses SSL/early TLS or that is willing to accept them on negotiation and that is part of the cardholder data environment as a security control needs to be changed such that it will only use TLS 1.1 (with an approved cipher suite) or above.
You need to recompile under .Net 4.5 or greater (TLS 1.2 is not enabled by default so code changes are needed) or use a 3rd party library that supports the required protocols.
Note that if you know your system is using SSL/early TLS you must created a risk mitigation plan/document.