Run the script to reorganize all indexes in all user databases.
We needed a script we can run while the systems are up and running , since rebuild only only works in Enterprise we had to resort to reorganizing indexes.
Widely followed practice is to ignore fragmentation for indexes with page counts < 1000 and re organize for indexes where fragmentation < 30% and rebuild where fragmentation > 30%. You can get index fragmentation info using sys.dm_db_index_physical_stats.