The problem of aggregating fuzzy structures, mainly fuzzy binary relations, has deserved a lot of attention in the last years due to its application in several fields. Here, we face the problem of studying which properties must satisfy a function in order to merge an arbitrary family of (bases of) L-probabilistic quasi-uniformities into a single one. These fuzzy structures are special filters of fuzzy binary relations. Hence we first make a complete study of functions between partially-ordered sets that preserve some special sets, such as filters. Afterwards, a complete characterization of those functions aggregating bases of L-probabilistic quasi-uniformities is obtained. In particular, attention is paid to the case L={0,1}, which allows one to obtain results for functions which aggregate crisp quasi-uniformities. Moreover, we provide some examples of our results including one showing that Lowen’s functor ι which transforms a probabilistic quasi-uniformity into a crisp quasi-uniformity can be constructed using this aggregation procedure.