" rel="stylesheet" />

When Linux antivirus lets you down: How to remove malware from a website manually - Page 2 - Manual search cookbook

Page 2 of 2

Manual search cookbook

In Linux and some Unix-like systems, it is hard to find more useful commands for searching files than find and grep

This command will look for all files that were modified in the past week.

find . -name '*.ph*' -mtime -7 

Sometimes, attackers change file modification dates to avoid detection. In this case, you can use the following command to look for .php and .phtml files that have had their attributes changed.

find . -name '*.ph*' -ctime -7 

If you need to look for file changes in a certain time frame, you can also use this find command.

find . -name '*.ph*' -newermt 2015-01-25 ! -newermt 2015-01-30 -ls 

And let's not underestimate the grep command as well. This command can recursively search for certain patterns in the files, drilling down through all folders and files. Here is an example.

grep -ril 'example.com/google-analytics/jquery-1.6.5.min.js' * 

When your web server is compromised, it is good practice to check files with the guid/suid flag, just to be safe.

sudo find / -perm -4000 -o -perm -2000 

Finally, you can use a command like this to identify what PHP scripts are currently running in the background and possibly impacting website performance.

lsof +r 1 -p `ps axww | grep httpd | grep -v grep | awk '{ if(!str) { str=$1 } else { str=str","}} END{print str}'` | grep vhosts | grep php 

Malicious code analysis

Now that we know how to search for possibly malicious files, let's dive a bit deeper and list what exactly we are looking for and where.

1. Check the upload, cache, tmp, backup, log, and images directories.

You need to check all directories that are used for file uploading. For example, with Joomla you should look for .php files in the ./images folder. There is a high chance that if you find something, it will be malicious. For WordPress it is worth checking the wp-content/uploads, backup and theme cache directories.

find ./images -name '*.ph*' 

2. Looking for files with weird names

Here are examples of strange file names to look out for: php, fyi.php, n2fd2.php. You should also look for unusual patterns in file names. For example:

    • File names comprising an odd and unreadable mixture of letters, numbers and symbols, e.g. srrfwz.php, ath.php, kirill.php, b374k.php.php, tryag.php.
    • Because many users rename files by appending the digit '1', look out for normal-looking file names that append numbers other than 1 to filename parts, e.g. index9.php, wp3-login.php.

3. Looking for files with unusual extensions.

Let's suppose you have a website based on the WordPress CMS. Files with extensions such as .py, .rb, .pl, .cgi, .so, .c, .phtml, or .php3 would be unusual for such types of websites. If scripts or files with these extensions are found, most probably these are hacker tools. There is a chance of a false alarm, but it is low.

4. Looking for files with non-standard attributes or creation dates.

As mentioned above, files with modified attributes are suspicious. For example, if all the .php files that were uploaded to the server via FTP/SFTP have the owner file attribute set to 'user', and you also see a number of files having this attribute set to 'www-data', then it is worth checking the latter. Also, check if the script creation date is earlier than the website creation date. You can use the command templates from the cookbook section to bake up your own search queries, and speed up or optimize them.

5. Looking for doorways using a large number of .html or .php files.

If a directory contains a few thousand .php or .html files, there is a high chance that this is a doorway. You can use the following command to find the top 50 directories with the highest file counts (if you have many hosting accounts and files on the server, it is better to use this command in the specific folder/home directory you would like to check to save some execution time):
find ./ -xdev -type d -print0 | while IFS= read -d '' dir; do echo "$(find "$dir" -maxdepth 1 -print0 | grep -zc .) $dir"; done | sort -rn | head -50 

 (Check this thread to find more details on the commands for checking directory file counts.)

Server logs can help

  • Dependent relations between the date and time when an email was sent (using details in the mail log and email message header), and access_log entries, help to determine how mail spam was sent out, and find the mailer script on the server.
  • FTP xferlog analysis helps to identify which files were uploaded or changed during the attack and by whom.
  • If your mail server and PHP settings are correctly configured you can find the name of the sender PHP script and the full path to it in your mail log or in the full email message header. This helps to quickly find and eliminate the source of spammy deliveries.
  • Some modern CMSs and plugins have more advanced defense techniques to proactively detect cyber attacks. Their logs might show if there was any attack and whether the CMS or plugin was able to protect itself or not.
  • The access_log and error_log files also allow you to track a hacker's actions, if you were able to identify the script names that were used, the IP address or the HTTP user agent (User-Agent). You can also check the POST request on the day the attack happened. Often, such checks allow you to find which malicious files were uploaded and which were already present before the attack.

Integrity checks

It is much easier to analyze attack vectors and look for malware scripts on websites if some security precautions were already made beforehand. Integrity checks help to identify the changes on the file system in a timely manner, and detect malicious activities quickly. The easiest and most effective way to perform such checks is by using version control systems such as git, SVN, or CVS. For example, with git, if you correctly configure the .gitignore file, the process of integrity checking comes down to executing two commands:

git status # check all changed files
git diff # find malicious code

This guarantees that you have a backup copy of your files, and allows you to quickly restore the website to a previous state. Experienced server administrators can also use inotify, tripwire, auditd and similar tools to track file and folder access and changes.

Unfortunately, it is not always possible to configure the version control system or any site integrity check services on a server. In the case of shared hosting, it is not possible to use a version control system or system services. To overcome this problem you can use CMS extensions, in the form of a plugin or a stand-alone script, to track file changes. Some CMSs (e.g. Bitrix or DLE) already have built-in integrity checks.

If the website is using custom scripts or is built with static HTML files, you can use the following shell command to make a snapshot of currently stored files:

ls -lahR > original_file.txt

If any malware threats occur you can create another snapshot and then compare them using any comparison software you like, for example, WinDiff, AraxisMerge Tool, BeyondCompare, the diff command (on Linux) or even compare snapshots online. 


In cases where antivirus solutions fail to clean a hacked website, it is useful to know how to do it yourself on the command line, with heuristics, and using built-in OS and CMS tools and features. Even with high-rate detection malware scanners such as ImunifyAV, being able to confirm the detection rates manually is an important, confidence-building skill.

ImunifyAV is the completely free antivirus and anti-malware scanner. Upgrade to ImunifyAV+ to access the built-in, one-click, fully automated cleanup feature, or get it as part of Imunify360's complete and comprehensive website security solution, which includes an intelligent WAF, IDS and IPS, Proactive Defense, automated kernel patch management and more. 

A post-hack survival guide: cleaning your website ...
Imunify360 reduces hacking attempts by 90%

Related Posts



No comments made yet. Be the first to submit a comment
Already Registered? Login Here
Monday, 18 January 2021

Captcha Image

By accepting you will be accessing a service provided by a third-party external to https://www.imunify360.com/