Are you facing Timeout Error for Table Level Script which makes extensive use of SQL SELECT statement???
To find the resolution to this problem, please try to run your query in SQL backend using query window.
Analyze the query and see how much time it is taking through SQL. If the fault is in query, you need to think of optimizing your query. If there is no problem with the query, then you can think of applying indexing just to make query execution quite faster.
If the problem persists even if you have followed above given steps, then the table level script may be trying to open a record which is currently in context and locked by CRM. In this case, you will need to write your Table Level Script with some arrangements or other way (you can try using WITH(NOLOCK) in your select query statement); or find alternative way to accomplish your requirement in order to reduce system overhead.