| Amira Script | amira Tcl script (rw) |
| Amira Script Object | amira custom module written in Tcl (rw) |
| AmiraMesh Format | amira's native general purpose format (rw) |
| AmiraMesh as LargeDiskData | access image data blockwise (r) |
| Analyze 7.5 | 3D image data with separate header file (rw) |
| AnalyzeAVW | contains 2D and 3D medical image data (rw) |
| BMP Image Format | uncompressed Windows bitmap format (rw) |
| DXF | Drawing Interchange Format for AutoCAD 3D models (rw) |
| Encapsulated PostScript | for 2D raster images only (w) |
| HTML | Hypertext document format (r) |
| HxSurface | amira's native format for triangular surfaces (rw) |
| Icol | ASCII format for colormaps with alpha channel (rw) |
| Interfile | Interfile file reader (r) |
| JPEG Image Format | 2D image format with lossy compression (rw) |
| MATLAB Binary Format (.mat) | MATLAB matrices (rw) |
| MATLAB M-files Format (.m) | MATLAB script (rw) |
| Open Inventor | standard file format for 3D models (rw) |
| PNG Image Format | portable network graphics format for 2D images (rw) |
| PNM Image Format | simple uncompressed 2D image format (rw) |
| PSI format | ASCII format for 3D points and associated data values (rw) |
| Ply Format | Stanford triangle format for points and surfaces (rw) |
| Raw Data | binary data as a 3D uniform field (rw) |
| Raw Data as LargeDiskData | access image data blockwise (r) |
| SGI-RGB Image Format | 2D image format with run-length encoding (rw) |
| STL | simple format for triangular surfaces, no connectivity (rw) |
| Stacked-Slices | info file grouping together 2D images (r) |
| TIFF Image Format | standard format for 2D and 3D image data (rw) |
| Tecplot | Tecplot ASCII and Binary file reader (r) |
| VRML | virtual reality markup language for 3D models (rw) |
| AMBER | Assisted Model Building with Energy Refinement format (r) |
| AMF | Amira Molecule Format (rw) |
| GROMACS | Groningen Machine for Chemical Simulations format (rw) |
| MDL | MDL file format saving chemical structures (rw) |
| PDB | protein data base file format (rw) |
| PSF/DCD (CHARMM) | file format used by CHARMM (r) |
| Tripos | file format used to save Tripos Sybyl molecules (rw) |
| UniChem | file format used by the UniChem molecular software (rw) |
| ZIB Molecular File Format | structured molecular file format (rw) |
| AmiraVR Config File | AmiraVR Config File (.cfg) |
| LDA | VolumeViz native file format (r) |
| LargeDiskData | access image data blockwise (rw) |
| Stacked-Slices as LargeDiskData | access image data blockwise (r) |
| AVS Field | stores data defined on regular grid (rw) |
| AVS UCD Format | stores unstructured cell data (rw) |
| FIDAP NEUTRAL | stores FEM meshes and solution data (r) |
| Fluent / UNS | contains FEM meshes, boundary ids, solution data (rw) |
| Hypermesh | used by Altair HyperWorks FEM software (rw) |
| IDEAS universal format | describes FEM grids and simulation data (rw) |
| Plot 3D Single Structured | stores curvilinear grids and associated data (rw) |
| CATIA4 | Computer Aided Three-dimensional Interactive Application V4 (r) |
| CATIA5 | Computer Aided Three-dimensional Interactive Application V5 (r) |
| ACR-NEMA | predecessor of the DICOM format for medical images (r) |
| DICOM | standard file format for medical images (rw) |
| IGES | Initial Graphics Exchange Specification (r) |
| Madymo | Madymo kinematics format (r) |
| Madymo Time-history | time-history output from Madymo (r) |
| Radioss | Mecalog Radioss format for simulations (r) |
| SEG-Y | Society of Exploration Geophysicists format Y (r) |
| STEP | Standard for The Exchange of Product data (r) |
| Bio-Rad Confocal Format | simple uncompressed format for 3D image stacks (r) |
| Leica 3D TIFF | contains 3D image data with voxel sizes (r) |
| Leica Binary Format (.lei) | 3D image stacks, time series, and meta information (r) |
| Leica Slice Series (.info) | contains list of 2D TIFF files and meta information (r) |
| MRC | MRC file format for electron microscopy (rw) |
| Metamorph STK Format | special TIFF variant for 3D image stacks (r) |
| Zeiss LSM | 3D raster image format (r) |