How to make website secure and hacker proof?

Websites are bargained all the time. Most of the website security breaches are not to take data or jumble with the website layout, but the attempts to use the server as an email transmit for spam, or to set up a momentary web server, generally to aid files of an illegal site. Other very usual methods to misuse compromised machinery is to use the servers as part of a botnet. Hacking is often done by automatic scripts written to scrub the internet in an effort to exploit recognized website security issues in software.
Can you guys tell how to protect the website from security breach and hackers?