You can easily secure your files by storing them on any SharePoint site and making sure, the site has unique security settings. The content that is stored on a site (all document libraries, other web parts) inherit permissions from that site. Setting security at the site level is considered the best practice in SharePoint.
There might be a situation when you need to store files on a SharePoint site (say project site) but have unique security for a handful of those files. If this is the case, you might want to create an extra document library and then break the permissions inheritance of that library. In such case, the site as a whole will be accessible by all who need to have access to it, yet, the document library will have unique privileges in terms of security.
You can also just store your sensitive content in your own OneDrive account. By default, it is private, until you share and you can easily control who you are sharing with from within your OneDrive (works the same way as sharing from SharePoint). To learn more about sharing from OneDrive, check out this post. Of course, one thing to keep in mind is that OneDrive is tied to your user ID, so if you win a lottery tomorrow and decide not to show up at work, your files are going to be deleted with the account, leaving your jealous co-workers without those important files that should have been in SharePoint, to begin with. (source)
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