Some how I managed to get the updates done.. though it took really long long time.. I could not make it any faster.
Mat_role_id was indexed.

But now I want to do a delete:
delete from mwebmatrix where mat_category = 2000;
To make it faster I am doing it in batches like..
delete from mwebmatrix where mat_category = 2000 and mat_id <500000;

mat_id is PK and mat_category is FK and indexed.

I am the only one using this database at this time and this is the only query I will be running. Do you think dropping the index on mat_category will make it faster ?

thanks