As Java developer, you are probably using a lot of frameworks. Spring or Hibernate can significantly reduce amount of boilerplate code. But inversion of control, dependency injections and proxies can be confusing during debugging. It is often annoying when debugger steps into third party library code. You realize that your code is wired via proxies and you have to add breakpoint into code you expect to hit.
But there is better way in Eclipse. Feature called Step Filtering. Very few of my former and current colleagues using Eclipse were aware of it. Just go into Window -> Preferences and search for Step Filtering. Check Use Step Filters and specify packages/classes you want to skip during debugging.