This is a good article I have read on reindexing a sql 2000 DB. It has some basic steps you can take as well as some more in-depth steps that will work better on large databases.
The easiest way is to setup a SQL Server maintenance plan. These plans can be configured to rebuild the indexes of your database. Do keep in mind that when reindexing the database users will not be able to access the database so the reindex should be done off hours. You also have the option of defragging the indexes. After you do the initial rebuild of the indexes you should look into defraging them weekly or so to keep them healthy.
The end result between defragging the indexes and rebuilding them is the same. The difference is that lightly indexes will defrag faster than they will rebuild. The command to defrag an index is “DBCC INDEXDEFRAG” and the command to rebuild an index is “DBCC DBREINDEX”.