We thank the reviewer for their comments and recommendations on our manuscript. The reviewer raises a number of valid points that we addressed in the main text as follows:

L6 and L32: This phrasing was used to discern between the location (spatial information) of the grains and the size (dimensional information) of the grains. This has been clarified in the text.

Fig. 1 and L27f: This has been changed to ‘surface magnetometry data with CT data’ to clarify that two datasets are being used.

Fig. 2: The sentence about scaling has been adjusted. The sample shown is an example image from a different study, used to illustrate the type of data used in MMT.

L95f: It is true that the surface roughness can be affected by the mineralogy. However, the marker structures adhere well to the entire sample, which contains a mixture of minerals typical for a basalt. We therefore do not distinguish between which minerals are suitable for mask structures and which are not. The total assemblage works well, as long as it is properly polished according to geological thin section polishing standards.

Fig. 4: This has been adjusted.

L110: An explanation has been added.

L116: The sample holder is cooled with water to keep the temperature of the substrate low enough. While there is no temperature sensor available in the particular setup used in this work, we know from other setups where a sensor is included on the sample holder that the sample holder’s temperature does not heat up to temperatures over 50°C. To give a more specific upper bound for the sputter setup used in this work, we note that another common resist used is PMMA (polymethacrylate). PMMA has a glass temperature of 105°C, which means that if the temperature of the sample would exceed that temperature, the resist would start to flow and features printed into the resist by lithography would be compromised. We do never observe this effect (even for much longer exposure to the Ar-plasma in longer etching/deposition processes). The magnetic interference of the heating is therefore considered to be negligible.

L168:  The LED of the QDM and the magnetic surface map of the QDM share a coordinate system, because they are obtained with the same camera. We co-register the CT data to the QDM data, which can be complicated. Therefore we need the marker structures. This has been clarified in the text.

L175: This should indeed be ‘width’ and has been adjusted in the text.

L170: This has been adjusted in the text.

L174f and Fig. 5a-b: This is indeed incorrect. These are optical microscopy images; this has been adjusted in the text.

L199f: There are practical problems in applying a thicker Nb-layer. Since it is quite a complicated and time-consuming procedure to apply the marker structures, we stayed on the safe side for this case study and only tried a thinner layer. However, because we experienced no problems whatsoever during the procedure, and because of the expertise and skills of the lab operator, we expect thicker layers to be possible with a bit of procedure optimization. This lies outside the scope of the current study. This has been clarified in the text.

L214: This is indeed incorrect and has been adjusted in the text.

L214f: The co-registration can be successfully achieved with the applied marker structures with a 50 µm width. When multiple structures are applied at known distances from one another, they provide a highly reliable reference system for aligning the datasets. The main improvement is that the co-registration process no longer depends on the presence of natural features on the samples, that are recognizable in both types of imaging. This ensures that co-registration is possible for every sample, including those where natural, recognizable features are insufficient. It is difficult to quantify the improvement in terms of pixel shift, because the outcome of co-registration is basically binary: it is possible, or it is not. This has been added to the text.

L55, L57, L173, L240: These suggestions have been implemented where needed.

We thank the reviewer for their constructive comments and recommendations. The points raised are relevant, and we have addressed them in the main text as follows:

1) The co-registration can be successfully achieved with the applied marker structures with a 50 µm width. When multiple structures are applied at known distances from one another, they provide a highly reliable reference system for aligning the datasets. The main improvement is that the co-registration process no longer depends on the presence of natural features on the samples, that are recognizable in both types of imaging. This ensures that co-registration is possible for every sample, including those where natural, recognizable features are insufficient. This has been added to the text.

2) This has been added to the discussion.

3) Microlithography is a well-established technique in fields such as the semiconductor industry. As demonstrated in our study, laboratories equipped for this type of research can readily apply the method to geological samples as well. In terms of accessibility, the costs are not exceedingly high when compared to the costs of high-end microscopy such as SEM or nanoCT, with which this approach is intended to be combined for co-registration. If no microlithography facilities are available to a user in the field, alternative options are available as outlined in the discussion, although they come with their own limitations.

4) The instruments used for the different imaging techniques in this study are fundamentally different. The QDM is camera-based and the CT scanner relies on an X-ray detector. Although both instruments are properly calibrated, they acquire data in very different ways. In practice, this inevitably leads to mismatches in field of view and resolution, complicating accurate co-registration.

5) Generally, heating below 100°C does not harm the magnetic signal, as this temperature is typically below the temperature range of interest in paleomagnetic research. For example, samples in our lab are routinely heated to this temperature to remove any surface contamination. However, if the low temperature magnetic behavior of a sample is the point of interest, it is important to consider the potential effects of heating. This has been clarified in the text.

6) The table lists the parameters that can be adjusted as part of the measurement configuration. These include source current and source voltage.

7) It is indeed true that resolution and voxel size are not the same, this has been clarified in the text.