We have to put correct codes in .htaccess file to work CMS's properly. Otherwise the internal links may through 'file not found error' while accessing the websites. Here I am pasting the default code for Drupal CMS. The installation folder for Drupal contains the .htaccess file. If not, create the file with proper ownership.
Paste the below code:
#######
# Apache/PHP/Drupal settings:
#
# Protect files and directories from prying eyes.
<FilesMatch
"\.(engine|inc|info|install|make|module|profile|test|po|sh|.*sql|theme|tpl(\.php)?|xtmpl)(~|\.sw[op]|\.bak|\.orig|\.save)?$|^(\..*|Entries.*|Repository|Root|Tag|Template|composer\.(json|lock))$|^#.*#$|\.php(~|\.sw[op]|\.bak|\.orig\.save)$">
Order allow,deny
# Don't show directory listings for URLs which map to a directory.
Options -Indexes
# Follow symbolic links in this directory.
Options +FollowSymLinks
# Make Drupal handle any 404 errors.
ErrorDocument 404 /index.php
# Set the default handler.
DirectoryIndex index.php index.html index.htm
# Override PHP settings that cannot be changed at runtime. See
# sites/default/default.settings.php and drupal_environment_initialize() in
# includes/bootstrap.inc for settings that can be changed at runtime.
# PHP 5, Apache 1 and 2.
php_flag magic_quotes_gpcoff
php_flag magic_quotes_sybaseoff
php_flag register_globalsoff
php_flag session.auto_startoff
php_value mbstring.http_inputpass
php_value mbstring.http_outputpass
php_flag mbstring.encoding_translationoff
# Requires mod_expires to be enabled.
# Enable expirations.
ExpiresActive On
# Cache all files for 2 weeks after access (A).
ExpiresDefault A1209600
# Do not allow PHP scripts to be cached unless they explicitly send cache
# headers themselves. Otherwise all scripts would have to overwrite the
# headers set by mod_expires if they want another caching behavior. This may
# fail if an error occurs early in the bootstrap process, and it may cause
# problems if a non-Drupal PHP file is installed in a subdirectory.
ExpiresActive Off
# Various rewrite rules.
RewriteEngine on
# Set "protossl" to "s" if we were accessed via https://.This is used later
# if you enable "www." stripping or enforcement, in order to ensure that
# you don't bounce between http and https.
RewriteRule ^ - [E=protossl]
RewriteCond %{HTTPS} on
RewriteRule ^ - [E=protossl:s]
# Make sure Authorization HTTP header is available to PHP
# even when running as CGI or FastCGI.
RewriteRule ^ - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
# Block access to "hidden" directories whose names begin with a period. This
# includes directories used by version control systems such as Subversion or
# Git to store control files. Files whose names begin with a period, as well
# as the control files used by CVS, are protected by the FilesMatch directive
# above.
#
# NOTE: This only works when mod_rewrite is loaded. Without mod_rewrite, it is
# not possible to block access to entire directories from .htaccess, because
#is not allowed here.
#
# If you do not have mod_rewrite installed, you should remove these
# directories from your webroot or otherwise protect them from being
# downloaded.
RewriteRule "(^|/)\." - [F]
# If your site can be accessed both with and without the 'www.' prefix, you
# can use one of the following settings to redirect users to your preferred
# URL, either WITH or WITHOUT the 'www.' prefix. Choose ONLY one option:
#
# To redirect all users to access the site WITH the 'www.' prefix,
# (http://example.com/... will be redirected to http://www.example.com/...)
# uncomment the following:
# RewriteCond %{HTTP_HOST} .
# RewriteCond %{HTTP_HOST} !^www\. [NC]
# RewriteRule ^ http%{ENV:protossl}://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]
#
# To redirect all users to access the site WITHOUT the 'www.' prefix,
# (http://www.example.com/... will be redirected to http://example.com/...)
# uncomment the following:
# RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
# RewriteRule ^ http%{ENV:protossl}://%1%{REQUEST_URI} [L,R=301]
# Modify the RewriteBase if you are using Drupal in a subdirectory or in a
# VirtualDocumentRoot and the rewrite rules are not working properly.
# For example if your site is at http://example.com/drupal uncomment and
# modify the following line:
# RewriteBase /drupal
#
# If your site is running in a VirtualDocumentRoot at http://example.com/,
# uncomment the following line:
# RewriteBase /
# Pass all requests not referring directly to files in the filesystem to
# index.php. Clean URLs are handled in drupal_environment_initialize().
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^ index.php [L]
# Rules to correctly serve gzip compressed CSS and JS files.
# Requires both mod_rewrite and mod_headers to be enabled.
# Serve gzip compressed CSS files if they exist and the client accepts gzip.
RewriteCond %{HTTP:Accept-encoding} gzip
RewriteCond %{REQUEST_FILENAME}\.gz -s
RewriteRule ^(.*)\.css $1\.css\.gz [QSA]
# Serve gzip compressed JS files if they exist and the client accepts gzip.
RewriteCond %{HTTP:Accept-encoding} gzip
RewriteCond %{REQUEST_FILENAME}\.gz -s
RewriteRule ^(.*)\.js $1\.js\.gz [QSA]
# Serve correct content types, and prevent mod_deflate double gzip.
RewriteRule \.css\.gz$ - [T=text/css,E=no-gzip:1]
RewriteRule \.js\.gz$ - [T=text/javascript,E=no-gzip:1]
<FilesMatch "(\.js\.gz|\.css\.gz)$">
# Serve correct encoding type.
Header set Content-Encoding gzip
# Force proxies to cache gzipped & non-gzipped css/js files separately.
Header append Vary Accept-Encoding
# Add headers to all responses.
# Disable content sniffing, since it's an attack vector.
Header always set X-Content-Type-Options nosniff
#######