This page is intended to act as a repository for manuals for atomic force microscopes. At this time, there is relatively little information here (basically, the manuals I have .pdf copies of), but I hope that over time it will grow. If you have a manual for your instrument that you think could be useful for other AFM users, please send it to me at This email address is being protected from spambots. You need JavaScript enabled to view it..


I hope that this page is useful for AFM users, especially those who inherited older instruments that have become spearated 



  • TT2-AFM manual v2.3 - This .pdf file is the user manual for AFMWorkshop's 2nd gen TT-AFM , i.e. "Table-Top AFM"
  •  LS-AFM Manual v1.1 - This user manual is for AFMWorkshop's "Life Sciences AFM". This covers the AFM instrument, there may be a separate manual for the optical microscope from AFM Workshop if you have a copy of that one, please send it to me
  •  HR-AFM Manual - This .pdf file is the user manual for AFMWorkshop's "High Resolution AFM" instrument. Unlike the TT2 manual, it covers use of the v4.x software
  •  B-AFM Manual v1.0 - This is the user maual for the B-AFM from AFMWorkshop


Asylum Research (now  Oxford Instruments)

  • MFP 3D User Guide V13 - This is the .pdf file of the user guide for the MFP 3D Bio-AFM from Asylum which was since aquired by Oxford Instruments
  • Cypher User Guide -  This is the User guide for the Cypher "small sample AFM", from Asylum



  • Nanoscope Software 6.13 User Guide - This .pdf file is the user manual for the nanoscope software interface for any microscope using a nanoscope controller, i.e. the popular multimode and dimension instruments. This version is compatible with Windows XP latest.
  • Multimode Instruction Manual v4.31 - This is a .pdf version of the instruction manual for the multimode microscope. This is based on a rather old version of the software (in DOS windows). Note that for these DI instruments, the controller and microscope have spearate manuals.


JPK (now a part of Bruker)

  • Nanowizard User Manual - This .pdf file is the user manual for JPK (now Bruker) Nanowizard bio-AFM instruments. THis covers the version 6.0 software. As far as I know this means instruments up to Nanowizard 4. Covers hardware, control software and analysis functions.


 Molecular Imaging/Agilent/Keysight

  • Agilent 5500 User Guide revB - This .pdf is the user guide for the Agilent 5500 microscope, which I think used to be called the PicoPlus before it becasme an Agilent instrument


Other Documents

A Practical Guide to Scanning Probe Microscopy - This is a .pdf file of the SPM practical guide, which I beleive was first made by TopoMetrix, this is the Thermomicroscopes version. This is a very old document, but contains a lot of helpful information for AFM users, still. Not an instrument manual, it's a simple guide to the general principles of how an AFM works. If you read this and want something more in-depth, I reccomend this book!



During July 2020, the AFMBiomed summer school series was supposed to take place in Marseille, France. Due to CoVID travel restrictions, the course took place online. However, since, there was no travel involved, and because the organizers kindly decided to make signup free, the school, had a record number of participants. At times 300 people were online, which is amazing for a specialized course like this, and showed just how many people around the world want to learn about and improve their AFM!

The lecturers were really great, and despite working in this field for 20 years, even I learned some things! Since I thought the material was so good, I am including links to the archived lectures below. The "tutorial" lectures were particularly good. Note that although the overall topic was "Biomedical Science", there are techniques here that could be useful for any AFM user.


This link contains the lectures in .pdf format:


Here You can find many of the lectures posted as videos on this site:


I highlight here some of the video tutorials that I found really useful: 





Please note that these video are published with a DOI record, therefore, it would be helpful to the authors if you cite them. I found this online class really great, and hope it returns!



  • Unfortunately, due to the coronavirus pandemic, we were unable to run the course on the proposed dates, so it's been postponed indefinitely.


Please click the image below to download the flyer with more details.

link to .pdf file of 2020 course flyer




 A blog with information and student feedback from the previous courses can be seen here:2017 course, 2014 course2013 course2011 course.

The course is supported by AFMWorkshop, The Faculty of Sciences of The University of Porto and my research institution, LAQV/Requimte

I recently wrote an application note on using AFM to characterize two-dimensional materials for AFMWorkshop. The full article can be found here. What follows is a brief extract.


Two dimensional materials are currently under development with potential to gain enormous importance in electronics, sensing, optics and other areas. Such materials, despite facile production methods in many cases, can display radically different properties compared to 3D or bulk materials. These new and enhanced properties come about due to nanoscale confinement effects, meaning they are generally accessible only when a material is limited to one, or at most to a few atomic layers. For this reason, research and development in 2D material and 2D materials-based devices relies crucially on the ability to characterise such materials at the nanoscale, including the observation of atomic steps. Atomic Force Microscopes are ideally suited for creating 3-D images and measurements on 2-D materials. This is because AFMs have extreme contrast on flat samples and can magnify surface heights by factors of millions to billions. AFM is unique in its ability to measure sample heights with resolution in excess of 0.1 nm. This explains why AFM has become a key tool in the arsenal of researchers studying 2D materials - for example, see the two images of layered materials below.




Figure 1a: Three dimensional color scaled image of SiC. The steps on this sample are 750 picometers.

Figure 1b: Colourscale image of HOPG, showing atomic steps.


Besides illustrating the power of an AFM, these types of samples serve as calibration samples for microscopes used for imaging 2-D materials.


Graphene is an extraordinary new two-dimensional material, consisting of single atomic layers of sp2 carbon. Although graphene is a single atom thick sheet, it is not typically found to be perfectly flat. Indeed, some nanometre scale corrugations, are commonly observed and may increase the stability of the 2D lattice. Despite its great strength, graphene is also a highly flexible material, and typically takes on the form of the underlying substrate. So, for example, on Si/SiO2 wafers, graphene can exhibit a considerable roughness due to the underlying substrate. Thus, a considerable texture, dependent on the SiO2 structure at the wafer surface, can be seen in the CVD graphene flakes shown in the left image in figure 2 below.



Figure 2. Examples of AFM images of CVD graphene deposited on Si/SiO2 wafers. Left: Single-layer graphene on a silicon wafer. In this example, the effect of the underlying texture on the graphene sheet is clearly seen. Right: Multilayer graphene of a silicon wafer. Arrows highlight some wrinkle-like defects, typical of CVD graphene.



To read more about AFM applications to two-dimensional materials, read the full application note here.

AFM Manufacturer list

The following is a simple alphabetical list of, hopefully, all the AFM manufacturers in the world. If you have any additions to make, get in touch via the contact form. For AFM probes, look at the SPM Probes list, and for reference samples, see the SPM References list. Note: I have moved the companies that are no longer separate businesses to a new list, below.