In filemanager you can select file on lefthand side.
With search filter active it is not possible anymore. Please make files selectable with options like:
-Select/deselect all
-Copy selected to different folder
-Delete selected

I have thousands of files, how can I remove a specific file? oh my goodness.

This would very welcome addition and improvement to the File Manager.

The search function in the File Manager works really great. It's an easy and quick way to search for specific files. Much, much faster than clicking through all directories to find a file. 

As a server administrator I use it quite often myself and I know many of my hosting customers are using it a lot too. The absence of file options (to delete, move or copy files) when using the search function is a real loss. As currently a user who has found a file (or multiple files) with search function has to clear the search first, remember the path where the files were found, navigate manually to those directories and delete (or move, or copy) the files one by one. Which very cumbersome.

Having the option to delete, move or copy files directly for searched file would make to experience much easier and quicker.

I have several directories in my web app that have hundreds of files in them. There are regularly occasions where I need to update or backup a group of files that share a common naming scheme. I can search for them in 10 seconds. But because I am unable to select them and perform bulk operations, I cannot operate on them as a group. Instead, I have to operate on them without the benefit of search which can take me 30 minutes of scrolling and selecting by hand. Wasting 30 minutes several times a week in what should be a trivial task is an unnecessary drain on resources.

Besides, what is the use case for having a search without the ability to invoke actions on the search targets? It always seemed to me that someone just didn't finish the search feature.

I extremely agree!!!!

and I extremely agree

I extremely agree