If you wish to remove the files from the project, the API does not provide a method for that.
You can delete files using System.IO like Florentina suggests but you also need to tell Studio / the filebased project about it. You can achieve that by manipulating the project XML itself.
But be careful: before you do that, you first need to unload it from Studio. So what you would do is
var controller = SdlTradosStudio.Application.GetController<ProjectsController>();
var pPath = project.FilePath;
Then load sdlproj file as XmlDocument() or XDocument,
var projectXML = new XmlDocument();
carefully remove the respective nodes from the ProjectFiles node (make sure to remove both source and target language files), save, reopen:
project = new FileBasedProject(pPath);