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In the modern world, english is a well-estabilished technical and scientific language. Some terms have become so commonly used that they are accepted in my native tongue (words like "computer", "PC", "network" being examples).

I'm currently writing a science fiction novel in my native language. I deal a lot with themes like networking, artificial intelligence, computing and so on in the novel.

So, when the time comes to create make up words for very specific technologies (let's say, nanomachines), it feels normal to use english-looking words (in the example, nano-mechs).

Considering the science fiction setting, is this acceptable or alienating?

I think it is important to write what your intended readers will easily understand. If you are a native speaker and inclined toward English-sounding words; they are probably inclined to understand that perfectly, so go ahead.

Otherwise, using your native language, you create a cognitive dissonance; namely how did YOUR language come to be the one used for such a technology, when everywhere in the world, English is the default language for technology, for academic papers, for engineering, etc.

Use what will probably be used; and if you don't, write a brief explanation for how some other language came to be used.

Seems totally fine to me. However, what really matters is your actual audience. This sounds like a case where maybe the best approach is to go ahead, write what seems best to you, without worrying too much about it--but then seek the responses of a sufficient number of representative beta readers. Even if you could very convincingly argue what the "right" approach is, what would it matter if the result sounded bad to the ears of your intended audience? (I remember this issue being discussed in the writing excuses podcast; if you search for "beta readers" you'll probably find several useful episodes.)

Is your novel set in future?

Generally speaking, yes. It is both reasonable and safe to assume that English will continue to serve as a primary language of scientific and engineering community. Thus, most new terms would be based on English.

Even though this may turn out to be false, selecting a different language is a controversial decision. For example, you may supplant English by Mandarin Chinese, but that would make your novel to stand out. While it may be received well in China, international success would be harder to achieve.

Supplanting English with your native language may also depend on how books are usually translated. It is easier if translators to your language have a tradition of replacing English terms with local equivalents, and harder if the tradition is to keep those terms verbatim.