I would argue that the modern idea of defining a countries as a contiguous territory with well-defined borders, was not dominant during the Middle Ages. Before the modern era, in Europe at least, a monarch's territory was more like a list of places, e.g. I own this county, that city, that village, and so on.
We can corroborate by looking at recent treaties vs historical ones.
Let's look at an example from the Peace of Westphalia (1648), this is even after what scholars considered the Middle ages.
LXXI. First, That the chief Dominion, Right of Sovereignty, and all other
Rights upon the Bishopricks of Metz, Toul, and Verdun, and on the
Citys of that Name and their Diocesses, particularly on Mayenvick, in
the same manner they formerly belong'd to the Emperor, shall for the
future appertain to the Crown of France, and shall be irrevocably
incorporated therewith for ever, saving the Right of the Metropolitan,
which belongs to the Archbishop of Treves.
Note that bishoprics and cities are named but not where the borders are. In fact, the treaty doesn't seem to imagine that there are borders at all. Where are the limits of the "Bishoprick of Metz"? I assume that this is determined by local practices. Other provisions about who owns what are also in this manner.
The Treaty of Tordesillas (1494) did famously define exact borders, but this method of definition were initially only used for territories and colonies outside Europe and not for Europe only. Not to mention the impossibility of marking the borders defined in that treaty.
Compare with the modern day Treaty of Versailles:
The boundaries of Germany will be determined as follows:
1. With Belgium
From the point common to the three frontiers of Belgium, Holland, and Germany and in a southerly direction:
the north-eastern boundary of the former territory of neutral Moresnet
then the eastern boundary of the Kreis of Eupen, then the frontier
between Belgium and the Kreis of Montjoie, then the northeastern and
eastern boundary of the Kreis of Malmedy to its junction with the
frontier of Luxemburg.
First of all, the treaty explicitly mentions "boundaries". It still mentions places like the "Kreis of Eupen" and "Kreis of Montjoie", but not in terms of A owns X and B owns Y, but just as reference points to determine exact borders. The borders with Poland (not pasted here, for brevity) are defined in an even more exact and detailed manner.
As promised, here are some scholarly sources that support this view:
For example, Alexander Diener and Joshua Hagen wrote in Borders: A Very Short Introduction (Oxford University Press, 2012)
Although some familiar names, like France and England, could be found on Europe's map at the time, these entities were structured quite differently than their modern successors. Instead of distinct sovereign states, medieval Europe was organized around what became known as the feudal system. [...] Marriages and land transactions between noble families, elaborate inheritance customs, and military conquest further complicated the situation. [...] Given this confused structure, precise territorial borders were not necessarily needed or helpful so long as taxes were collected, services rendered, and oaths fulfilled especially in sparsely populated areas. (p. 38, emphasis mine)
Or Alex Anievas and Kerem Nisancioglu in How the West Came to Rule, (Pluto Press, 2015)
In the Old World, treaties concluding wars typically emphasised nonlinear or noncontiguous territoriality, and the spoils of conquests were divided according to places rather than territories. [...] The first examples of linearly defined claims to political authority can be found in the 1493 Papal Bulls and the 1494 Treaty of Tordesillas between Spain and Portugal. (p.137, emphasis mine)
So, my answer to your question is that the concept of "borders" was not very important in Europe during the Middle Ages, so I doubt that there were practices of formally marking borders.