Remove index.php from Magento shop urls.

Magento shop on 1.9.3.7


All our pages seem to have ‘index.php’ inserted into them. We would like this removed to display only the intended URLs and the site to be tested for full functionality afterwards.

We've already attempted the quick fix for this (by going into the CMS... system>config>web>search engine optimisation> setting web rewrites to ‘yes’. and pasting some recommended lines into the .htaccess file. But this only partially worked and users were getting a blank white page when trying to access the checkout). Following that I reversed what I had done.
Pref. the work the work carried out outside of peak UK hours I’d also like a maintenance page up while to job's being done.