Hello Danniella,
Yes, the situation is similar in Arabic (and in Malagasy for verbs and Korean for suffixes). You can use 'morphological dictionary graphs' (user's manual, Section 3.8.4). In the dictionary of nouns, don't add the prefixes. In the graph, create a path with the prefix and another without the prefix. Declare the dictionary of nouns as 'morphological-mode dictionary'. When you apply the dictionaries to the text ('Apply lexical resources' in the Text menu), apply the graph (.fst2) instead of the dictionary of nouns (.bin).
This method allows you also to take into account compatibility/incompatibility between some prefixes and some nouns, and morphological variations of prefixes or nouns in contact with each other.
Best wishes,
Eric Laporte