A Markdown document may open in Obsidian while its illustrations are missing. The note was imported, but the files its links refer to were left behind. Treat a PDF-to-Markdown result as content plus any resources it actually uses, not automatically as one self-contained text file.
The workflow below uses Obsidian as an external notes app. PDF Craft does not automatically synchronize your export into a vault.
Inspect the download before moving it
Download the completed Markdown result from PDF Craft and inspect what you received. If it is an archive, extract it first. Identify the main Markdown document and check whether it references local resources, remote URLs, or both. Do not assume every conversion uses the same folder names.
Open the .md file in a text editor and find an image reference. Its target tells you which resources must travel with it. A path such as images/figure-1.png is relative to that Markdown file; it is not an instruction for Obsidian to download the original PDF's figures automatically.
Retain an untouched copy of the download. If a move or renaming step breaks links, you can compare with the original structure instead of converting the PDF again.
Put the document in a deliberate vault location
Choose a folder for the source material, such as one folder per paper or book. Obsidian's Markdown import documentation describes adding files through its file explorer or copying them into the vault with your system's file browser. Follow the method supported on your device.
Move the Markdown and its necessary resources together while preserving their relative structure. Avoid collecting every project's image into one directory with filenames such as image1.png; identical names can collide or become hard to trace.
Obsidian also has attachment-location settings for newly added attachments. Those settings do not mean every existing path in imported Markdown has been rewritten. Check the actual imported references before reorganizing a resource folder.
Check headings, links, and pictures inside the vault
Open the note in reading view and inspect its outline. Headings should describe the source's sections, not every repeated page header. Then follow an internal section link, a note reference, and an external citation.
Look at one image near the start and one later in the document. Compare each caption and figure reference with the original PDF. A thumbnail appearing in the note is not proof that the full image or its important labels are intact.
If a picture fails to appear, inspect the link's case, extension, and folder location. Determine whether it expects a local file or a network request. Do not fix a broken local path by silently replacing it with an unrelated web image.
For supported attachment behavior, consult Obsidian's attachment guide. For the broader file-handling problem, use Markdown image assets.
Keep quotations connected to the source PDF
Add a brief source note containing title, authors or publisher, edition or date, original filename, and relevant page locations. If printed page labels differ from the PDF viewer's count, record the distinction.
Keep the source PDF in a stable location you can access from your research workflow. If it lives outside the vault, consider what happens when you move the vault to another device. A working link on one computer may not resolve elsewhere.
Before quoting a converted passage, compare it with the PDF. OCR errors can be indexed and retrieved just as successfully as correct text. A searchable note is not automatically a verified quotation.
Turn the import into useful notes after checking it
Once the source note works, create shorter notes for the ideas you need. Carry over the source and page reference rather than pasting isolated claims into unrelated files.
For a table, retain its heading, units, and any qualifying note. For a formula, check both the expression and the destination renderer before relying on it. Do not let cleanup turn an uncertain passage into an apparently settled fact.
The PDF-to-Markdown research workflow and scanned-book notes guide describe that next stage. First get a reproducible import: the note, resources, and route back to the PDF should still work after you close and reopen the vault.