WordPress will create an .htaccess file automatically if you are using Permalinks. There will not be an .htaccess file if Permalinks are set to default, unless another component has created it. WordPress will only look to the one single instance of .htaccess in the WP root (unless you specifically setup a separate sub-folder install) and ignore any versions in sub folders.
Try testing for the folder layers you want to remove with a RewriteCond check and then rewrite those up to root or up one layer, whichever is your goal.
Something like this should produce what you are looking for:
RewriteEngine on
#
# stuff to let through (ignore)
RewriteCond %{REQUEST_URI} "/folder1/" [OR]
RewriteCond %{REQUEST_URI} "/folder2/"
RewriteRule (.*) $1 [L]
More details about this approach here and from Apache directly