What are the methods to make a project estimation more accurate?

The best method I believe is the bottom-up, but needs experience as Rahul said.

There is no short cut other than experience.

to increase the accuracy of your estimation the following should be done:

1- Quantity take offs.

2- Project documents and specification to be thoroughly studied.

3- Receive quotations from the vendors for non common items.

4- refer to your procurement rates on previous projects for similar items.

5- cross check the price with previous similar tender submitted and where was your price with reference to your competitors.

6- After project award to have a feed back from the operation team for the cost performance, which is usually done via a Cost Control Department.

To follow bottom up estimation

Bottom up estimation with expert judgement/advise.

To make your direct cost estimation as accurate as possible , you will need to do the following

1. Proper quantities (if there is buffer you will need to know the percentages)

2. Accurate wastage factors

3. Current market rates.

4. Productivity and operation norms of major equipments

5. Time Cycles

6. Site visit with your logistics plan.

with these tools you can do a proper direct cost estimate.