This is a Canonical Question about Securing a LAMP stack
What are the absolute guidelines for securing a LAMP server?
David's answer is a good baseline of the general principles of server hardening. As David indicated, this is a huge question. The specific techniques you take could depend highly on your environment and how your server will be used. Warning, this can take a lot of work in a test environment to build out and get done right. Followed by a lot of work to integrate into your production environment, and more importantly, business process.
First, however, check to see if your organization has any hardening policies, as those might be the most directly relevant. If not, depending on your role, this might be a great time to build them out. I would also recommend tackling each component separately from the bottom up.
You've asked a question that is, quite frankly, worthy of a few books on the topic. But there are some general basic guidelines that work well:
Hope that helps you get started.