Check to see if the files referenced in your logs are files that you think exist or should exist on your site. If the files are files that you think should be on your site, then you might have some incorrect links in some of you pages. You can use a web crawler to check this.
If the pages referred to in the messages are things like ".../cmd.exe" or other pages that are not and never were on your site, then these log entries probably represent probes from bots looking for known exploits in some versions of some web servers. There is not much you can do about this. Welcome to the Internet.
If the client address for many of the requests is the same over a period of an hour or more, you are best advised to block that particular IP address at your external firewall.