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Just a few corrections from a native speaker: the "über-" prefix is in fact used in many other words. Über- and unter- are the direct German equivalents to the english super- and sub-, respectively.

Some valid uses of the prefix, with no racist implications whatsoever: Überbrücken (override), Übereiffer (overzealousness), überarbeiten (overworking), übernatürlich (supernatural).

Über as a descriptive word can also be used just like the English "over" - "Die Kuh sprang über den Mond" - "The cow jumped over the moon".

While the term "Übermensch" has gained racist connotation through the Nazi period in some contexts, any other usages of the word über should not be worried about. (for those interested, "Übermensch" is the literal translation of "super-human").