Restored from TM now Unix folder show in root directory

I had to do a install from a complete time machine backup which had a few hiccups but that was mostly programs that are sandboxed that did not like to be installed from a time machine backup so I reinstalled them all is working fine.
I did however come to notice that in my root directory " /  " I have visible Unix folders such as:
bin
cores
opt
private
sbin
( Alias ) User Information
usr
Volumes
The file
mach_Kernel
I would think these files would start with a period and hence would not show with the normal folders, Applications, Library, System, and Users and if I am correct how do I go about change them so they are recognized as files that should be there just not visible to me?
If there is something else I should know please let me know.
I would think the visibility attributes are not set correctly for the folders and the one file and one alias folder.
Looking into terminal commands I would think setfile command would be what I am looking for but I need help making sure the command I would like to issue on the folder, files and alias is correct.
I have basically come up with this command set after reading the man setfile
SetFile -P -a -V (folder name)
I am just not sure it the -P is correct as in man it say that -P acts on a symlink file instead on the file the symlink resolves to.
The files do not appear to be symlinks with the exceptions of the User Information folder.
Any one help me with this?
Thank you.
Leon

To hide all fies that should be invisible you can use this command then press return.
defaults write com.apple.finder AppleShowAllFiles False; killall Finder
To Hide individual files or folders
sudo chflags hidden
Then drag the file or folder you want hidden to your Terminal window.
It will now show the path to the item.
Press Return.

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