The Professor's Trunk
The Professor's Trunk is an item that appears throughout the whole Professor Layton Series. It serves as a main menu to the games, containing various options that aid Professor Layton and Luke on their investigations, such as a Save function and a Puzzle Index. In the prequel trilogy, the trunk is not able to be used until Layton gives Luke and Emmy a tutorial on how to use it. From the beginning of each game, three silhouetted options appear, which later turn into mini-games. Commonly, seven options appear in the trunk in the first three games, and eight in the prequel trilogy.
 Layton's Journal
Layton's Journal contains a list of journal entries written by Professor Layton, which details progress on each investigation. This can be used by the player to reflect back on the investigation, essentially serving as a summary of the story of each game. In Professor Layton vs. Phoenix Wright: Ace Attorney, this option is simply known as Story.
Alongside the main investigation, each game contains a list of ten mysteries (twelve in Azran Legacy) when, once solved, will aid with the investigation. Mysteries are gradually added and solved over the course of the game, and each are accompanied by a few of Professor Layton's thoughts.
 Puzzle Index
Once a puzzle is solved, it becomes part of the Puzzle Index, so that the player can try solving puzzles more than once. Each puzzle displays what type of puzzle it is, as well as the location in where it was solved, and in later games it also displays the number of Picarats it is worth and how many hints it took to solve. Unsolved puzzles are also added to the index, however they cannot be solved unless the player goes back to its original location. Puzzles can also be marked as a favorite and are included in a list of Picks.
This is where the player can save their progress. Each game contains three save files, and cannot be deleted unless the player overwrites it with a new save file. Each save file displays the player's current location, number of puzzles solved, number of Picarats obtained and number of hours clocked.
From the beginning of the game, three silhouetted icons appear in the trunk and cannot be accessed. These options are different mini-games that can be found within each game, and become accessible once each mini-game is obtained by a certain character. These mini-games, once completed, unlock different "houses" within Professor Layton's Challenges, holding additional puzzles to solve.
Beginning from Last Specter, the player can view special episodes in the trunk through progressing the story. These episodes usually give more insight on particular characters or parts of the investigation, and are not mandatory to view.
As well as the addition of Episodes, Last Specter also introduced a Collection feature, which serves as a display for many trinkets that are found throughout each games. Each collection item can be viewed here, as well as Layton's description of it. Toward the beginning of each game Aldus gives the player an explanation of the collection feature, and awards the player the collection box.
Starting from Unwound Future, a Memo function was included to the trunk, serving a similar purpose to the Memo function within puzzles. Players can note down any findings within the Memo function, which can be shared between all save files on the one cartridge.
 Game Exclusive Features
 Old Diary
In Diabolical Box, Professor Layton and Luke come across an old diary belonging to Anton Herzen in Folsense, covered with locks. Once found, this becomes a feature in the trunk. Layton and Luke must find all the keys around Folsense to unlock different diary entries. The diary details Anton's life in Folsense and with Sophia, up until the day she leaves the town.
 London Life
In the US version of Last Specter, an RPG style game was included alongside the main game, in the form of London Life. The player can create their own character, fulfilling requests of the various characters from all previous games. The game was not included in European versions of the game due to localizing reasons.
 World Times
The World Times was introduced in Azran Legacy, and keeps a list of articles from around the world which Layton and the others obtain during their travels. These articles are written by Dariya Kolum, and act as side quests to unlock additional puzzles, areas to explore, and collection items.
 Treasure Hunt
Also introduced to Azran Legacy was Treasure Hunt mode, which utilizes the StreetPass feature of the 3DS. The player must find various objects around the world to add to their list. These items can be used to set challenges for other players. Once a challenge has been completed, the player will receive a number of points depending on the difficulty.
Introduced in Professor Layton vs. Phoenix Wright: Ace Attorney, the Items option keeps a record of all the items the main characters obtain through the game, similar to the Collection feature in the main series games. These items can be useful in trials, and will often be added to the Court Record for each appropriate trial.
The options feature is also exclusive to Professor Layton vs. Phoenix Wright: Ace Attorney. Here, the player is able to adjust the volume of the background music, sound effects, and voices. There is also a button which allows the player to reset these values to their default settings, should they be altered.