Yes and no is frustratingly the answer. I have just set up a brand new MacBook Pro. Because it was brand new and because I had a clone of my old MBP on a USB backup drive, rather than a Time Machine backup, I elected to do what you are proposing. That is, transfer my apps and files individually.
How to do this differs dependant on the app.
I found for Apple App Store apps it is easier to simply download them again from the Purchases page of the App Store.
Some apps from other sources can be reinstalled from the .dmg installer originally downloaded.
Some of these will require a user name and password to activate and should be uninstalled from the old machine using the provided uninstaller first especially if the licence is limited to one or two devices. MS Office is a good example.
Browsers like Google Chrome can be downloaded as new and if you have a Google account everything will be the same, bookmarks, extensions and passwords.
Files and folders can be copied directly from one drive to another.
All this may seem complex but it does leave behind a lot of accumulated baggage, some of which are simply outdated or unnecessary preferences and some which may slow or cause conflicts on your device. Most preferences will need to be reset.
It may sound a little complex but really it isn't. Essential apps and functions can be transferred in a few hours. The rest can be done as needed over a week or less.
You may find many apps you had before are unnecessary or you may find yourself using a native app instead that does the job as well or better.
BUT, I could have just used my cloning app, Carbon Copy Cloner to copy the clone back onto the new machine. A two step process which would have reproduced my old laptop on the new one. Everything the same nothing to do. This is fine if the clone is of the current Operating System, not so fine if you are updating your device and upgrading your OS at the same time from OSX 10.6.8 to El Capitan 10.11.6 either way a clone will allow you to pick and choose but where possible download new copies of your apps.
Sent from my iPhone using Mac Forums