Yes, you are using The an awful lot but do not worry, because I doubt that is a problem. That is normal and perhaps unavoidable. An astute readership will probably notice something is missing if you try to avoid it too often. I base these assumptions off of the fact that The is the absolute most regularly occurring word in the Contemporary Corpus of American English, and the fact that the so-called articles have an entire category of speech dedicated to them in the traditional system of categorization described by Robert Lowth in A Short Introduction to English Grammar, Grammar-land by M.L. Nesbit and even through to this day by many institutions, e.g. The University of Victoria, as well as most dictionaries. As such my primary suggestion is to actually not change your style of writing and desensitize yourself to it, because you may be trying to fix what is not broken and risk breaking it further. I suspect there may be other reasons you are just beginning to notice this now, but this is neither the time, nor the place to attempt to speculate or console regarding that issue. If you feel compelled to try and fix it nevertheless, I do have a suggestion. It is the same suggestion that people employ when they feel words are being overused in other situations. Use the closest synonym possible.
Regarding which words may be considered synonyms, I would note that some grammarians like Noah Webster1 and perhaps Leonard Bloomfield2 have criticized the traditional placement of words, and perhaps with rather good reason. These grammarians have broadened the lexical category and renamed it. Most grammarians of this type seem to use the word determiner to describe this category. According to the Farlex Grammar Book, Volume 1 English Grammar:
Determiners are used to introduce a noun or noun phrase. There are several classes of determiners: articles, demonstrative adjectives, possessive adjectives, interrogative adjectives, distributive determiners, pre-determiners, quantifiers, and numbers.
Determiners do two things. First, they signal that a noun or noun phrase will follow. Then, they give information about the item. They may tell us whether the item is general or specific, near or far, singular or plural; they can also quantify the item, describing how much or how many are referred to; or they can tell us to whom the item belongs.
The Farlex Grammar Book classifies the words This, That and The as determiners and they can all serve a very similar function. They specify a specific singular thing already mentioned. Consider these primary definitions from The Cambridge Academic Content Dictionary:
The: used before a noun to refer to a particular thing because it is clear which thing is intended:
This: used for a person, object, or thing to show which one is referred to or has been referred to before:
That: Used to refer to a person, object, event, etc., separated from the speaker by distance or time, or to something that has been referred to before, or to point to a particular thing:
There are slightly different connotations for each, and the plurality of meanings the words This, That and The are not always interchangeable, especially since This and That can also be classified as pronouns instead. As a matter of fact, despite The Farlex Book of Grammar classifying this, that, these and those as relative adjectives, they are more often called demonstrative pronouns as they are in English Grammar Today, which is published by Cambridge University Press and as pronouns they require antecedents. I suggest consulting your favorite dictionary for further details. Regardless, you might be able to use This and That as alternatives just often enough in order to alleviate your perturbed at how often the definite article (The grammarian's name for The, see O.A.L.D.) is used.
Speaking of pronouns, there are other determiners mentioned in the Farlex Book of Grammar too. Many of the words used as pronouns have the effect of a determiner and many of them are pronouns. You can see in the Farlex Book of Grammar that possessive nouns and pronouns are also determiners, and so we may sometimes use those in the place of The. This is relevant to your example sentences. Here are my suggested edits to your example sentences with knowledge:
The main purpose of the presented applications is to visualize roses in space.
The [Their] user[s] can run around and experience the roses from different angles. The position of the roses [roses' position] can be stored in the ROS-fileformat.
As you can see, two out of five instances of "the" in your example can be replaced with possessive pronouns, which represents a 40% reduction. You can achieve another 20% by using a quantifiers in the last sentence.
All roses/each rose/any number of roses/every rose can have their positions saved in the ROS-Fileformat
There is another of The I struck out, in the second of your exemplary sentence simply because it seems unnecessary to limit which roses a person can experience in the simulated environment. If you feel something is missing, you might want to try putting virtual or simulated there instead, as Noah Webster considered the determiners (which he called definitives) a subcategory of adjective instead of its own part of speech because they modify nouns by limiting them, which is something other adjectives like the ones I mentioned can do as well. Such adjectives are called qualifiers, which the 2010 Random House Webster's College Dictionary defines as "a word, as an adverb or adjective, that qualifies or limits the meaning of another; modifier." That same dictionary also has a definition of Determiner, which subcategories them as adjectives. Basically, whenever you would use "The" try to consider whether or not there are other ways to sufficiently restrict the noun's interpretation.
Incidentally, this situation reminds me of criticism jokes regarding the use of too many e's.
See Noah Webster's definitions for the words Article
in the 1828 American Dictionary of the English Language for a brief example. (Definitive is essentially the word he chose to call determiners, as he died before that word was ever used to describe this.)
2 This is a guess based on the fact that the O.E.D. 2 attests him as being the first to use the word determiner in its grammatical sense in 1933