restoring from Time Machine

I have read that App Delete (or may be it is App cleaner I cannot remember) app can remove certain things from the operating system .
This leads to a question if I have done a clean instal will then restoring from ~Time machine import the damaged system - I am not sure that it is damaged or is it safer to open Time machine disk on desktop and say import apps & docs but leave the library is this a way to avoid unwanted anomalies ? Can I just select individual apps by dragging them to the apps folder ?

Whenever I have restored from a Time Machine backup, it has restored the complete backup, including the OS, replacing everything on the hard drive from the backup.

So, I am not sure if it is possible to do a "restore" without replacing the whole system. Yes, it gives a very clear warning before it does that.

I have restored bits and pieces by opening time machine disk when mounted on the desktop including apps not all apps are available like Photo Booth but these could be pre Mavericks versions it asks for the password when restoring apps this way .
So as I put if I were to just reinstall specific items such as apps or things that are not on the other macs in the house it seems that I will be able to avoid some setting importation which avoids any passibility of corrupt files .
I assume that I have to make sure the new system is set up with the same name and master password otherwise the files will be closed to the new clean system .
I also suppose that if the system is set up with the original name and password then once again I could restore selected items through the normal Time Machine finder window.
It would of course be easier to restore from Time Machine after the system instal using the migrate program in the set up or in Utilities but I have found no mention of whether this will reinstall possible anomalies undoing the effect of a system wipe and fresh instal.
Is Time Machine clever enough to only copy the healthy files and settings ?

Franzleo, that's a good question. How could time machine know the good from the bad files? Checksum, perhaps? I doubt that much smarts are builtin to time machine. Please do let us know whatever you discover. I have a similar question.

Update:

Have you looked into the various Mac cleanup programs?

Such as:

tuneupmymac.com/Free-Mac-Cleaner
. . . "Gain Extra Space For Your Mac. Increase Mac Performance"

or

CCleaner?

Somewhere on this forum there must be a list with recommendations and reviews?

I cannot offer any help concerning individual app restoration from Time Machine, but I do strongly suggest only using ONYX to perform periodic maintenance on a Mac. Be sure to dl the appropriate version for your current OS.

I used to use onyx and some of the other maintenance programs I use one extra to Disk Utility now & that is Clean Genius Pro which is rapid to use. Disk Utility does all I need otherwise .
I once made the mistake of using MacCleaner and it told me I had lots of unnecessary files so I deleted them it turned out they were necessary they were system files I had to completely reinstall the OS .

As for the Time Machine question I think I will select by entering Time Machine & restoring apps & some documents that should avoid the possibility of importing compromised settings it will not be such an automated experience and will probable add some time to set the machine up how I like it but I see no harm in that .

Thanks for the tips. I recently upgraded from 750 GB to 1 TB internal hard drive on my MacBook Pro using time machine backup. I think a cleanup is in order. I have not done a "clean install" for years.. but am careful about installing anything that I don't really need. I just accumulate a lot of data as the years go by. Before I upgrade to Mavericks, I will need to go from 4GB to 8GB of RAM.

So, I will look into OxyX and Clean Genius Pro, and look for a guide or a list of similar tools to evaluate.