The current organisation of the manuscripts dates back to the librarian Johann Andreas Schmeller (1785 - 1852), who worked at the Court and State Library from 1829 to 1852. As far as such a thing was still possible 30 years after the main wave of secularisation, he attempted to reconstruct the collections of the former monastic libraries on the basis of their historical catalogues and then ordered the Latin manuscripts in a sequence of consecutive numbers according to the alphabetical order of their provenances, to form the Codices latini monacenses (Clm). Individual categories were also established for manuscripts in other languages (e. g. Cgm Codices germanici monacenses for the German manuscripts and Cod.graec. for the Greek manuscripts).

However, Schmeller did not manage to apply this method to the  Collection of Latin manuscripts. The Codices latini of the old court library kept their numbering from 1 to 698 or 701 to 947 a (later on continued to 967) originally introduced by Ignaz Hardt in 1806 and then continued by Schmeller. The numbers 1001 to 2500 were reserved for the Bavarian manuscripts of the court library. So far categorised as Codices bavarici 1 to 1329, these manuscripts became Cod. latini by adding the number 1000, so that Cod.bavar. 1 became Clm 1001 and Cod.bavar. 1329 became Clm 2329. The numbers 2330 to 2500 remained unallocated. Thus the works grouped as Bavarici latini remained together and were only provided with a cross-reference concerning their places of origin. Several thousand manuscripts, whose origin Schmeller had not managed to ascertain any more, were categorised as Codices incertae or diversae originis under the reference sign ZZ (Clm 23001 to 26279).

The section Clm 2501 to 22502 consequently contains the collections secularised or mediatised since 1802/03 in alphabetical order: Cod. Ab. (Carmelite Library Abensberg) became Clm 2501, Cod. Ab. 25 - the last manuscript from Abensberg - became Clm 2525. Schmeller organised his numbering in such a manner that at least the last digit of the Latin shelf mark corresponded to the last digit of the former "monastery shelf mark", which he achieved by leaving gaps in the numbering sequence. The former collections of the library of Aldersbach, alphabetically following Abensberg, thus start with the number 2531, not 2526. The numbering of the former collections of smaller libraries was started in increments of ten, whereas Schmeller preferred to start the numbering of larger collections with a round number, e. g. in the case of St. Emmeram with no. 14000, although the last preceding manuscript from the Regensburg seminary of Niedermuenster bears the number 13601.

In the printed catalogues by Karl Halm the Clm shelf mark is mentioned first, and the provenance shelf mark in brackets is printed next to it, e. g. Clm 18150 (= Teg. 150). It still makes sense to enter these shelf marks - which were intended merely as an interim measure by Schmeller - in a special  Concordance, since they were used in the older literature and in the source editions of the Monumenta Germaniae historica (MGH) until far into the late 19th century.

In the field of   Manuscripts in the German language the shelf marks Cgm 1 to 5154 represent the old holdings and the new acquisitions from the first half of the 19th century - thus the time of Schmeller. In contrast to the Latin manuscripts, the German manuscripts were not categorised according to provenance groups, but were shelved in a continuous series according to principles of form or content: The first 200 manuscripts are exclusively parchment manuscripts, the shelf marks Cgm 201 to 1499 represent the collection already held at the beginning of the 19th century, including many medieval manuscripts, which were primarily acquired in the course of secularisation. The section Cgm 1501 to 3587 contains the German-language Codices bavarici (formerly Cod.bav. 1501-3587), the holdings from Cgm 3601 to 5154 represent the rest of the old collections and new acquisitions under Schmeller, which were shelved according to size, and starting from Cgm 5155 the later new acquisitions were ordered chronologically according to their time of acquisition.