The goal is to find an element which can be applied remotely to a target (like from a laser), and work as a homing device for a missile. (Or at least, to find a homing device which could be applied remotely and would be undetectable to the target.)
The setting is a slightly more technologically advanced planet earth- roughly 50 years in the future. It's of course possible to fire missiles from aircraft which will target a particular building and blow it up.
However, there's a limit to how effective that can be since the buildings are also reinforced. The more powerful the bomb the more resources it takes to create and maintain them. Thus the shift in strategy is to make existing weapons more effective.
In the story, one nation has figured out a way. They send a scout to scope out the facility ahead of time. Using various technology (not relevant for this question) they can identify the weakest point on a structure from a few hundred meters away. For example, they can find a weak seam between two pieces of reinforced concrete. If you could have the missile hit exactly on that seam, it would be more effective at breaking through the reinforcements.
The problem is, how can the scout mark that spot from 200 meters away, such that when an airplane shoots a missile the homing device can lock onto that spot?
The initial idea was for the scout to have a machine capable of shooting a laser or particle beam on that specific weak spot. The beam would carry particles of a particular element and deposit them on that precise location in a very minute layer. The missiles would somehow be able to home in on that element and thus know where exactly to hit.
There are a few problems with this idea:
We couldn't find anything about a particle beam (or anything similar) which could transfer a layer of particles onto a surface. It seems like all the beams we currently have are meant to interact with the surface to create a new element, or to remove part of the surface (like an ion beam.) So we need to find the right way to transfer the particles.
In order for this to be effective, the scout needs to put something down which won't be noticeable for normal inspection. That means it can't make a visible mark. So even if the scout could effectively place a regular tracking device on a small area from 200 meters away (which would be almost impossible), the device couldn't be anything regular surveillance would pick up.
It needs to be something which a missile in the sky could lock on to. We were thinking at first of using a metallic element which is rare, and the missile could have a super-magnetic homing device which would only be magnetic for that specific metal. Alternatively, maybe it could be some sort of radioactive isotope which could be detected from the air.
The problem is figuring out what could create such a strong signal that an air-based device could identify it, without it being so obvious that the defense would pick it up.
So the question is:
What sort of homing mechanism can be identified by an air based missile, subtle enough that the ground defense wouldn't pick it up, and able to be precisely applied from a distance of 200 meters?
Obviously this question is based on pseudo-science; I haven't found (and don't expect to find) any actual examples of such materials. The goal is to find something which requires the least amount of bending science and sounds the most plausible- i.e. given current science, is there something which would answer the question and which readers would think could be realistic in 50 years?
edit: It was pointed out that targeting lasers do exist. The problem is it seems these only work if the laser is applied while the missile's in the air. I didn't find anything about the ability to mark a location which would be attacked at a later point.
(In the story, the scout would go around a large fortified compound and mark a dozen "weak spots" before leaving. Then, when the air assault starts, they could bomb away without needing any ground support.)