diff --git a/src/schema/applyRules.ts b/src/schema/applyRules.ts
index 568d8d48..2995c721 100644
--- a/src/schema/applyRules.ts
+++ b/src/schema/applyRules.ts
@@ -196,7 +196,7 @@ function evalJsonCheck(
   }
 
   const json: Record<string, unknown> = sidecarRule ? context.sidecar : context.json
-  for (const [key, requirement] of Object.entries(rule.fields)) {
+  for (const [key, requirement] of Object.entries(rule.fields ?? {})) {
     // @ts-expect-error dynamic nested index access on GenericSchema is not typed
     const metadataDef = schema.objects.metadata[key]
     const keyName: string = metadataDef.name
diff --git a/src/schema/pruneSchema.test.ts b/src/schema/pruneSchema.test.ts
new file mode 100644
index 00000000..dfa32157
--- /dev/null
+++ b/src/schema/pruneSchema.test.ts
@@ -0,0 +1,33 @@
+import { assert } from '@std/assert'
+import type { GenericRule, GenericSchema } from '../types/schema.ts'
+import { loadSchema } from '../setup/loadSchema.ts'
+import { pruneSchema, type SchemaFilter } from './pruneSchema.ts'
+
+Deno.test('Test schema pruning', async (t) => {
+  const schema = await loadSchema() as unknown as GenericSchema
+  await t.step('Test delete path', async () => {
+    const path = 'rules.sidecars'
+    const filter: SchemaFilter = {path}
+    assert(schema[path])
+    const newSchema = pruneSchema(schema, [filter])
+    assert(schema[path])
+    assert(newSchema[path] == undefined)
+  })
+  await t.step('Test delete matching rules', async () => {
+    const path = 'rules.sidecars'
+    const testPath = `${path}.derivatives.atlas.TemplateNonStandard`
+    const filter: SchemaFilter = {
+      path,
+      match: {
+        selectors: [
+          'dataset.dataset_description.DatasetType == "derivative"'
+        ]
+      }
+    }
+    assert(schema[testPath])
+    const newSchema = pruneSchema(schema, [filter])
+    assert(schema[path])
+    assert(schema[testPath])
+    assert(newSchema[testPath] == undefined)
+  })
+})
diff --git a/src/schema/pruneSchema.ts b/src/schema/pruneSchema.ts
new file mode 100644
index 00000000..809128fd
--- /dev/null
+++ b/src/schema/pruneSchema.ts
@@ -0,0 +1,67 @@
+import type { GenericRule, GenericSchema } from '../types/schema.ts'
+import { objectPathHandler } from '../utils/objectPathHandler.ts'
+
+export interface SchemaFilter {
+  path?: string,
+  match?: Partial<GenericRule>,
+  update?: Partial<GenericRule>
+}
+
+export function pruneSchema(
+  schema: GenericSchema,
+  filters: SchemaFilter[]
+): GenericSchema {
+  let newSchema = JSON.parse(JSON.stringify(schema))
+  newSchema = new Proxy( newSchema as object, objectPathHandler) as GenericSchema
+  filters.map(applyFilter.bind(null, newSchema))
+  return newSchema
+}
+
+function applyFilter(
+  schema: GenericSchema,
+  filter: SchemaFilter
+): GenericSchema {
+  if (filter.path && !filter.match) {
+    if (filter.update) {
+      Object.assign(schema[filter.path], filter.update)
+    } else {
+      delete schema[filter.path]
+    }
+    return schema 
+  }
+  const path = filter.path ?? 'rules'
+  _applyFilter(schema, filter, path)
+  return schema
+}
+
+function _applyFilter(
+  schema: GenericSchema,
+  filter: SchemaFilter,
+  path: string
+) {
+  if (typeof schema[path] != 'object') {
+    return
+  }
+  if (filter.match && ruleMatch(schema[path], filter.match)) {
+    if (filter.update) {
+      Object.assign(schema[path], filter.update)
+    } else {
+      delete schema[path]
+    }
+  }
+  for (const key in schema[path]) {
+    _applyFilter(schema, filter, `${path}.${key}`)
+  }
+  return
+}
+
+function ruleMatch(rule: GenericRule, match: Partial<GenericRule>): boolean {
+  return (Object.keys(match) as (keyof GenericRule)[]).every((key) => {
+    if (typeof rule[key] == 'undefined') return false
+    if (Array.isArray(match[key])) {
+      return match[key].every(entry => Array.isArray(rule[key]) && rule[key].includes(entry))
+    }
+    // TODO matches for rule fields that are strings or records
+    return false
+  })
+}
diff --git a/src/types/schema.ts b/src/types/schema.ts
index 9fdcba92..d40966c7 100644
--- a/src/types/schema.ts
+++ b/src/types/schema.ts
@@ -78,7 +78,7 @@ export interface GenericRule {
   columns?: Record<string, string>
   additional_columns?: string
   initial_columns?: string[]
-  fields: Record<string, SchemaFields>
+  fields?: Record<string, SchemaFields>
   issue?: SchemaIssue
   extensions?: string[]
   suffixes?: string[]
diff --git a/src/utils/objectPathHandler.ts b/src/utils/objectPathHandler.ts
index 8abaa525..6f17d72c 100644
--- a/src/utils/objectPathHandler.ts
+++ b/src/utils/objectPathHandler.ts
@@ -21,4 +21,23 @@ export const objectPathHandler = {
     }
     return res
   },
+  deleteProperty(target: unknown, property: string): boolean {
+    if (typeof property === 'symbol') {
+      return true
+    }
+    const props = property.split('.')
+    const toDelete = props.pop()
+    if (toDelete === undefined) {
+      return true
+    }
+    let parent = target
+    for (const prop of props) {
+      if (hasProp(parent, prop)) {
+        parent = parent[prop]
+      } else {
+        return true
+      }
+    }
+    return delete (parent as Record<string, unknown>)[toDelete]
+  }
 }