A method of preparing navigation of a tool to be used in a surgical intervention for treating a target region within the body of a patient, characterised in that it comprises the following steps: - Detecting the image position of a first reference marker disposed on the body of the patient by an image system, and detecting the spatial position of said first reference marker by a magnetic localizing system, wherein said first reference marker comprises: • a magnetic emitter or receiver having at least two coils arranged in a manner to define at least two vectors in a coordinate system of the magnetic localizing system; • a geometric element comprising hollow plastic tubes visible on image data of the imaging system and having a unique geometry detectable by the imaging system, - Calculating a first transform matrix between the image coordinate system of the imaging system and the spatial coordinate system associated with the first reference marker by using detected image and spatial positions of the first reference marker, in order to register data of the localizing system and imaging system together, - Detecting the spatial position of a pointer by the localizing system, - Constructing and displaying a navigation image, wherein a representation of the spatial position of the pointer is displayed on image data from the imaging system using the first transform matrix, - Determining an entry point and a trajectory allowing reaching the target region determined by using said representation of the pointer in the navigation image. - Detecting the image position of a first reference marker disposed on the body of the patient by an image system, and detecting the spatial position of said first reference marker by a magnetic localizing system, wherein said first reference marker comprises: • a magnetic emitter or receiver having at least two coils arranged in a manner to define at least two vectors in a coordinate system of the magnetic localizing system; • a geometric element comprising hollow plastic tubes visible on image data of the imaging system and having a unique geometry detectable by the imaging system, • a magnetic emitter or receiver having at least two coils arranged in a manner to define at least two vectors in a coordinate system of the magnetic localizing system; • a geometric element comprising hollow plastic tubes visible on image data of the imaging system and having a unique geometry detectable by the imaging system, - Calculating a first transform matrix between the image coordinate system of the imaging system and the spatial coordinate system associated with the first reference marker by using detected image and spatial positions of the first reference marker, in order to register data of the localizing system and imaging system together, - Detecting the spatial position of a pointer by the localizing system, - Constructing and displaying a navigation image, wherein a representation of the spatial position of the pointer is displayed on image data from the imaging system using the first transform matrix, - Determining an entry point and a trajectory allowing reaching the target region determined by using said representation of the pointer in the navigation image.