To re-index a single field, find the field definition in Manage | Database | Fields and double-click it. Use storage options to change it to an unindexed field. Click OK until you have exited Manage | Database. Then return to this field definition and turn indexing back on.
You can rebuild all the indexes in a file by importing all the records into a clone of the file or by using Recover in FileMaker 11 with only these options selected:
Copy File Blocks As Is.
Rebuild Field indexes now.