For CQ5.2X or CQ5.3 or upgraded CQ5.4 remove or rename following files or folder
In some cases you can also recreate indexes by deleting or renaming following folders and files (Some of the files and folder has nothing to do with index, they are just removed for cleaning purpose
For CQ5.4 / CRX2.2 / CQ5.5 / CRX2.3 remove or rename following files and folders
For AEM6 onward (If you are using oak MK), Rebuilding indexes can happen while system is running (Note that query would not run faster if you do reindex)
Please read https://docs.adobe.com/docs/en/aem/6-0/deploy/upgrade/queries-and-indexing.html and https://docs.adobe.com/docs/en/aem/6-1/deploy/best-practices/best-practices-for-queries-and-indexing.html before doing re indexing.
I think best way to do reindexing in AEM6 is to use this tool http://adobe-consulting-services.github.io/acs-aem-commons/features/oak-index-manager.html
for doing full indexing of repo in AEM6 you can set reindex to true at oak:index node. More info is here http://jackrabbit.apache.org/oak/docs/query.html
If you don't have access to install this tool then you can manually go to crxde repo and set reindex property to true for property you want to reindex (This is expensive operation, don't do it if you don't know what you are doing).
In some cases you need to stop your system remove/rename repository/index folder and then start instance again
Note: In some cases if your repository size is huge, It could take days to rebuild Lucene index. So Before you rebuild your index, make sure that you can afford that much of downtime.