The notion of "converting URLs" from one thing to another is completely ambiguous, see the top part of this answer for an explanation of what happens to URLs when redirecting or rewriting: https://stackoverflow.com/a/11711948/851273
There's 2 things that happen, and I'm going to take a wild stab and guess that you want the 2nd thing, since you're complaining that refreshing the page doesn't do anything.
When you type http://atwd/books/course?course_id=CC100&format=XML&submit=Submit
into your browser, this is the request URI that gets sent through mod_rewrite: /books/course
. In your rule, you are matching against a blank URI: RewriteRule ^$ /course/%1/format/%2 [R,L]
. That's the first reason your rule doesn't work. The second reason why it doesn't work is because above that, everything except images and index.php and robots.txt is being routed through index.php. So even if you were matching against the right URI, it gets routed before your rule even gets to do anything.
You need to correct the pattern in your rule to match the URI that you expect to redirect, and you need to place this rule before the routing rule that you have. So everything should look roughly like this:
<IfModule mod_rewrite.c>
RewriteEngine on
RewriteBase /
RewriteCond %{QUERY_STRING} ^course_id=([^&]+)&format=([^&]+)$
RewriteRule ^/?books/course$ /course/%1/format/%2 [R,L]
#Source: http://codeigniter.com/user_guide/general/urls.html
#Removal of index.php
RewriteCond $1 !^(index.php|images|robots.txt)
RewriteRule ^(.*)$ /index.php?route/$1 [L]
</IfModule>
You'll need to tweak the paths to make sure they match what you are actually looking for.
To both redirect the browser and internally rewrite back to your original URL, you need to do something different.
First, you need to make sure all of your links look like this: /course/CC100/format/XML
. Change your CMS or static HTML so all the links show up that way.
Then, you need to change the rules around (all before your codeigniter routing rule) to be something liek this:
<IfModule mod_rewrite.c>
RewriteEngine on
RewriteBase /
# redirect browser to a URI without the query string
RewriteCond %{THE_REQUEST} ^(GET|HEAD) /books/course/??course_id=([^&]+)&format=([^&]+)
RewriteRule ^/?books/course$ /course/%2/format/%3? [R,L]
# internally rewrite query string-less request back to one with query strings
RewriteRule ^/?course/([^/]+)/format/([^/]+)$ /books/course?course_id=$1&format=$2&submit=Submit [L]
#Source: http://codeigniter.com/user_guide/general/urls.html
#Removal of index.php
RewriteCond $1 !^(index.php|images|robots.txt)
RewriteRule ^(.*)$ /index.php?route/$1 [L]
</IfModule>
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