The Indexer in Eclipse CDT runs in the background indexing the source files of your project. Indexer is one of the main reasons Eclipse can be slow. You can see it churning away in the background most of the time.
If you have a lot of files in your project that you do not want to be indexed, that would ease the load on the indexer and make your Eclipse user experience better. To exclude such files from Indexer:
Go to project Properties -> C/C++ General -> Paths and Symbols.
Go to Source Location tab, click on your project name and choose Edit Filter.
In the Edit Filter dialog, add the files you want to be excluded from indexing.
Tried with: Eclipse 4.5 (Mars) and Ubuntu 14.04